Compositions and methods for the treatment of hemoglobinopathies

ABSTRACT

The present invention is directed to genome editing systems, reagents and methods for the treatment of hemoglobinopathies.

RELATED APPLICATIONS

This application claims priority to U.S. Provisional patent application No. 62/271,968, filed Dec. 28, 2015, and U.S. Provisional patent application No. 62/347,484, filed Jun. 8, 2016. The entire contents of these applications are incorporated herein by reference.

BACKGROUND

CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats) evolved in bacteria as an adaptive immune system to defend against viral attack. Upon exposure to a virus, short segments of viral DNA are integrated into the CRISPR locus of the bacterial genome. RNA is transcribed from a portion of the CRISPR locus that includes the viral sequence. That RNA, which contains sequence complimentary to the viral genome, mediates targeting of a Cas9 protein to the sequence in the viral genome. The Cas9 protein cleaves and thereby silences the viral target.

Recently, the CRISPR/Cas system has been adapted for genome editing in eukaryotic cells. The introduction of site-specific single (SSBs) or double strand breaks (DSBs) allows for target sequence alteration through, for example, non-homologous end joining (NHEJ) or homology-directed repair (HDR).

SUMMARY OF THE INVENTION

Without being bound by theory, the invention is based in part on the discovery that CRISPR systems, e.g., Cas9 CRISPR systems, e.g., as described herein, can be used to modify cells (e.g., hematopoietic stem and progenitor cells (HSPCs)) to increase fetal hemoglobin (HbF) expression and/or decrease expression of beta globin (e.g., a beta globin gene having a disease-causing mutation), and that such cells may be used to treat hemoglobinopathies, e.g., sickle cell disease and beta thalassemia.

Thus, in an aspect, the invention provides CRISPR systems (e.g., Cas CRISPR systems, e.g., Cas9 CRISPR systems, e.g., S. pyogenes Cas9 CRISPR systems) comprising one or more, e.g., one, gRNA molecule as described herein. Any of the gRNA molecules described herein may be used in such systems, and in the methods and cells described herein.

In an aspect, the invention provides a gRNA molecule that includes a tracr and crRNA, wherein the crRNA includes a targeting domain that is complementary with a target sequence of the BCL11A gene, a BCL11a enhancer, or a HFPH region.

In another aspect, the invention provides a gRNA molecule that includes a targeting domain that is complementary with a target sequence of the BCL11A gene, e.g., is complementary with a target sequence within a BCL11a coding region (e.g., within a BCL11a exon, e.g., within BCL11a exon 2). In embodiments, the gRNA comprises a targeting domain that includes, e.g., consists of, any one of SEQ ID NO: 1 to SEQ ID NO: 85 or SEQ ID NO: 400 to SEQ ID NO: 1231.

In another aspect, the invention provides a gRNA molecule that includes a targeting domain that is complementary with a target sequence of a BCL11A enhancer.

In embodiments, the gRNA comprises a targeting domain that includes, e.g., consists of, any one of SEQ ID NO: 1232 to SEQ ID NO: 1499.

In embodiments, the gRNA to a target sequence of a BCL11a enhancer is to a target sequence within the +58 region of the BCL11a enhancer, and the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 182 to SEQ ID NO: 277 or SEQ ID NO: 334 to SEQ ID NO: 341. In embodiments, the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 341, SEQ ID NO: 246, SEQ ID NO: 248, SEQ ID NO: 247, SEQ ID NO: 245, SEQ ID NO: 249, SEQ ID NO: 244, SEQ ID NO: 199, SEQ ID NO: 251, SEQ ID NO: 250, SEQ ID NO: 334, SEQ ID NO: 185, SEQ ID NO: 186, SEQ ID NO: 336, or SEQ ID NO: 337. In embodiments, the targeting domain includes, e.g., consists of, SEQ ID NO: 248. In embodiments, the targeting domain includes, e.g., consists of, SEQ ID NO: 247. In embodiments, the targeting domain includes, e.g., consists of, SEQ ID NO: 245. In embodiments, the targeting domain includes, e.g., consists of, SEQ ID NO: 336. In embodiments, the targeting domain includes, e.g., consists of, SEQ ID NO: 337. In embodiments, the targeting domain includes, e.g., consists of, SEQ ID NO: 338. In embodiments, the targeting domain includes, e.g., consists of, SEQ ID NO: 335. In embodiments, the targeting domain includes, e.g., consists of, SEQ ID NO: 252. In an embodiment, the gRNA is a dgRNA that includes a crRNA that includes, e.g., consists of, e.g., from 5′ to 3′, SEQ ID NO: 248-SEQ ID NO: 6607, and a tracr that includes, e.g., consists of, e.g., from 5′ to 3′, SEQ ID NO: 6660. In an embodiment, the gRNA is a dgRNA that includes a crRNA that includes, e.g., consists of, e.g., from 5′ to 3′, SEQ ID NO: 247-SEQ ID NO: 6607, and a tracr that includes, e.g., consists of, e.g., from 5′ to 3′, SEQ ID NO: 6660. In an embodiment, the gRNA molecule is a sgRNA molecule and includes, e.g., consists of, e.g., from 5′ to 3′, SEQ ID NO: 338-SEQ ID NO: 6604-UUUU. In an embodiment, the gRNA molecule is a sgRNA molecule and includes, e.g., consists of, e.g., from 5′ to 3′, SEQ ID NO: 335-SEQ ID NO: 6604-UUUU. In an embodiment, the gRNA molecule is a sgRNA molecule and includes, e.g., consists of, e.g., from 5′ to 3′, SEQ ID NO: 336-SEQ ID NO: 6604-UUUU. In an embodiment, the gRNA molecule is a sgRNA molecule and includes, e.g., consists of, e.g., from 5′ to 3′, SEQ ID NO: 245-SEQ ID NO: 6604-UUUU. In an embodiment, the gRNA molecule is a sgRNA molecule and includes, e.g., consists of, e.g., from 5′ to 3′, SEQ ID NO: 337-SEQ ID NO: 6604-UUUU. In an embodiment, the gRNA molecule is a sgRNA molecule and includes, e.g., consists of, e.g., from 5′ to 3′, SEQ ID NO: 252-SEQ ID NO: 6604-UUUU.

In embodiments, the gRNA to a target sequence of a BCL11a enhancer is to a target sequence within the +62 region of the BCL11a enhancer, and the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 278 to SEQ ID NO: 333. In embodiments, the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 318, SEQ ID NO: 312, SEQ ID NO: 313, SEQ ID NO: 294, SEQ ID NO: 310, SEQ ID NO: 319, SEQ ID NO: 298, SEQ ID NO: 322, SEQ ID NO: 311, SEQ ID NO: 315, SEQ ID NO: 290, SEQ ID NO: 317, SEQ ID NO: 309, SEQ ID NO: 289, or SEQ ID NO: 281. In embodiments, the targeting domain includes, e.g., consists of, SEQ ID NO: 318.

In embodiments, the gRNA to a target sequence of a BCL11a enhancer is to a target sequence within the +55 region of the BCL11a enhancer, and the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 1596 to SEQ ID NO: 1691. In embodiments, the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 1683, SEQ ID NO: 1638, SEQ ID NO: 1647, SEQ ID NO: 1609, SEQ ID NO: 1621, SEQ ID NO: 1617, SEQ ID NO: 1654, SEQ ID NO: 1631, SEQ ID NO: 1620, SEQ ID NO: 1637, SEQ ID NO: 1612, SEQ ID NO: 1656, SEQ ID NO: 1619, SEQ ID NO: 1675, SEQ ID NO: 1645, SEQ ID NO: 1598, SEQ ID NO: 1599, SEQ ID NO: 1663, SEQ ID NO: 1677, or SEQ ID NO: 1626.

In another aspect, the invention provides a gRNA molecule that includes a targeting domain that is complementary with a target sequence of a hereditary persistence of fetal hemoglobin (HPFH) region. In an embodiment, the HPFH region is the French HPFH region. In embodiments, the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 86 to SEQ ID NO: 181 or SEQ ID NO: 1500 to SEQ ID NO: 1595. In embodiments, the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 100, SEQ ID NO: 165, SEQ ID NO: 113, SEQ ID NO: 99, SEQ ID NO: 112, SEQ ID NO: 98, SEQ ID NO: 1580, SEQ ID NO: 106, SEQ ID NO: 1503, SEQ ID NO: 1589, SEQ ID NO: 160, SEQ ID NO: 1537, SEQ ID NO: 159, SEQ ID NO: 101, SEQ ID NO: 162, SEQ ID NO: 104, SEQ ID NO: 138, SEQ ID NO: 1536, SEQ ID NO: 1539, SEQ ID NO: 1585. In embodiments, the targeting domain includes, e.g., consists of, SEQ ID NO: 100. In embodiments, the targeting domain includes, e.g., consists of, SEQ ID NO: 165. In embodiments, the targeting domain includes, e.g., consists of, SEQ ID NO: 113.

In any of the aforementioned embodiments, the gRNA molecule may further have regions and/or properties described herein. In an aspect, the gRNA molecule (e.g., of any of the aforementioned aspects or embodiments) includes a targeting domain that includes, e.g., consists of, 17, 18, 19, 20, 21, 22, 23, or 24 consecutive nucleic acids of any one of the recited targeting domain sequences. In embodiments, the 17, 18, 19, 20, 21, 22, 23, or 24 consecutive nucleic acids of any one of the recited targeting domain sequences are the 17, 18, 19, 20, 21, 22, 23, or 24 consecutive nucleic acids disposed at the 3′ end of the recited targeting domain sequence. In embodiments, the 17, 18, 19, 20, 21, 22, 23, or 24 consecutive nucleic acids of any one of the recited targeting domain sequences are the 17, 18, 19, 20, 21, 22, 23, or 24 consecutive nucleic acids disposed at the 5′ end of the recited targeting domain sequence. In embodiments, the 17, 18, 19, 20, 21, 22, 23, or 24 consecutive nucleic acids of any one of the recited targeting domain sequences do not include either the 5′ or 3′ nucleic acid of the recited targeting domain sequence. In any of the aforementioned aspects or embodiments, the targeting domain may consist of the recited targeting domain sequence.

In embodiments of the gRNA molecule, including in any of the aforementioned aspects and embodiments, the targeting domain includes 17, 18, 19, 20, 21 (if present in the reference sequence), 22 (if present in the reference sequence), 23 (if present in the reference sequence), 24 (if present in the reference sequence), or 25 (if present in the reference sequence) consecutive nucleic acids of any one of the recited targeting domain sequences. In other embodiments of the gRNA molecule, including in any of the aforementioned aspects and embodiments, the targeting domain consists of 17, 18, 19, 20, 21 (if present in the reference sequence), 22 (if present in the reference sequence), 23 (if present in the reference sequence), or 24 (if present in the reference sequence), or 25 (if present in the reference sequence) consecutive nucleic acids of any one of the recited targeting domain sequences. In embodiments of the gRNA molecule, including in any of the aforementioned aspects and embodiments, the 17, 18, 19, 20, 21 (if present in the reference sequence), 22 (if present in the reference sequence), 23 (if present in the reference sequence), or 24 (if present in the reference sequence), or 25 (if present in the reference sequence) consecutive nucleic acids of any one of the recited targeting domain sequences are the 17, 18, 19, 20, 21 (if present in the reference sequence), 22 (if present in the reference sequence), 23 (if present in the reference sequence), or 24 (if present in the reference sequence), or 25 (if present in the reference sequence) consecutive nucleic acids disposed at the 3′ end of the recited targeting domain sequence. In other embodiments of the gRNA molecule, including in any of the aforementioned aspects and embodiments, the 17, 18, 19, 20, 21 (if present in the reference sequence), 22 (if present in the reference sequence), 23 (if present in the reference sequence), or 24 (if present in the reference sequence), or 25 (if present in the reference sequence) consecutive nucleic acids of any one of the recited targeting domain sequences are the 17, 18, 19, 20, 21 (if present in the reference sequence), 22 (if present in the reference sequence), 23 (if present in the reference sequence), or 24 (if present in the reference sequence), or 25 (if present in the reference sequence) consecutive nucleic acids disposed at the 5′ end of the recited targeting domain sequence. In other embodiments of the gRNA molecule, including in any of the aforementioned aspects and embodiments, the 17, 18, 19, 20, 21 (if present in the reference sequence), 22 (if present in the reference sequence), 23 (if present in the reference sequence), or 24 (if present in the reference sequence), or 25 (if present in the reference sequence) consecutive nucleic acids of any one of the recited targeting domain sequences do not include either the 5′ or 3′ nucleic acid of the recited targeting domain sequence.

In an aspect, including in any of the aforementioned aspects or embodiments, the gRNA molecule includes a portion of the crRNA and a portion of the tracr that hybridize to form a flagpole, that includes SEQ ID NO: 6584 or 6585. In embodiments, the flagpole further includes a first flagpole extension, located 3′ to the crRNA portion of the flagpole, wherein said first flagpole extension includes SEQ ID NO: 6586. In embodiments, the flagpole further includes a second flagpole extension located 3′ to the crRNA portion of the flagpole and, if present, the first flagpole extension, wherein said second flagpole extension includes SEQ ID NO: 6587.

In an aspect, including in any of the aforementioned aspects or embodiments, the invention provides a gRNA molecule that includes a tracr that includes, e.g., consists of, SEQ ID NO: 6660 or SEQ ID NO: 6661. In embodiments, the crRNA portion of the flagpole includes SEQ ID NO: 6607 or SEQ ID NO: 6608.

In an aspect, including in any of the aforementioned aspects or embodiments, the invention provides a gRNA molecule that includes a tracr that includes SEQ ID NO: 6589 or 6590, and optionally, if a first flagpole extension is present, a first tracr extension, disposed 5′ to SEQ ID NO: 6589 or 6590, said first tracr extension including SEQ ID NO: 6591.

In an aspect, including in any of the aforementioned aspects or embodiments, the invention provides a gRNA molecule wherein the targeting domain and the tracr are disposed on separate nucleic acid molecules (e.g., a dgRNA molecule).

In an aspect, including in any of the aforementioned aspects or embodiments, the invention provides a gRNA molecule wherein the targeting domain and the tracr are disposed on a single nucleic acid molecule (e.g., a sgRNA molecule), and wherein the tracr is disposed 3′ to the targeting domain. In embodiments, the sgRNA molecule includes a loop, disposed 3′ to the targeting domain and 5′ to the tracr, e.g., a loop including, e.g., consisting of, SEQ ID NO: 6588.

In an aspect, including in any of the aforementioned aspects or embodiments, the invention provides a gRNA molecule including, from 5′ to 3′, [targeting domain]-:

(a) SEQ ID NO: 6601; (b) SEQ ID NO: 6602; (c) SEQ ID NO: 6603; (d) SEQ ID NO: 6604; or

(e) any of (a) to (d), above, further including, at the 3′ end, 1, 2, 3, 4, 5, 6 or 7 uracil (U) nucleotides, e.g., 4 uracil nucleotides. In embodiments, there are no intervening nucleotides between the targeting domain and the sequence of any of (a)-(e).

In another aspect, the invention provides CRISPR systems, e.g., Cas CRISPR systems, e.g., Cas9 CRISPR systems, e.g., S. pyogenes Cas9 CRISPR systems, the include one or more, e.g., one, gRNA molecule of any of the aforementioned aspects and embodiments. In an aspect, the invention provides a composition including a first gRNA molecule of any of the aforementioned aspects and embodiments, further including a Cas9 molecule. In embodiments, the Cas9 molecule is an active or inactive s. pyogenes Cas9. In embodiments, the first gRNA molecule and Cas9 molecule are present in a ribonuclear protein complex (RNP).

In another aspect, the invention provides compositions that include more than one gRNA, e.g., more than one gRNA molecule as described herein, e.g., more than one gRNA molecule of any of the aforementioned gRNA molecule aspects or embodiments. Thus, in a further aspect, the invention provides a composition of any of the aforementioned composition aspects and embodiments, further including a second gRNA molecule; a second gRNA molecule and a third gRNA molecule; or a second gRNA molecule, a third gRNA molecule, and a fourth gRNA molecule, wherein the second gRNA molecule, the third gRNA molecule (if present), and the fourth gRNA molecule (if present) are a gRNA molecule as described herein, e.g., a gRNA molecule of any of the aforementioned gRNA molecule aspects or embodiments. In an embodiment, each gRNA molecule of the composition is complementary to a different target sequence. In an embodiment, each gRNA molecule is complementary to target sequences within the same gene or region. In an aspect, the first gRNA molecule, the second gRNA molecule, the third gRNA molecule (if present), and the fourth gRNA molecule (if present) are complementary to target sequences not more than 20000 nucleotides, not more than 10000 nucleotides, not more than 6000, not more than 5000 nucleotides, not more than 4000, not more than 1000 nucleotides, not more than 500 nucleotides, not more than 400 nucleotides, not more than 300 nucleotides, not more than 200 nucleotides, not more than 100 nucleotides, not more than 90 nucleotides, not more than 80 nucleotides, not more than 70 nucleotides, not more than 60 nucleotides, not more than 50 nucleotides, not more than 40 nucleotides, not more than 30 nucleotides, not more than 20 nucleotides or not more than 10 nucleotides apart. In another aspect, each gRNA molecule of the composition is complementary to target sequence within a different gene or region.

Specific and preferred combinations of more than one gRNA molecule of the invention are described herein. In an aspect, the composition includes a first gRNA molecule and a second gRNA molecule, wherein the first gRNA molecule and second gRNA molecule are complementary to different target sequences, and are:

(a) independently selected from the gRNA molecules described herein (e.g., above) to the BCL11a gene; (b) independently selected from the gRNA molecules described herein (e.g., above) to the +58 BCL11a enhancer; (c) independently selected from the gRNA molecules described herein (e.g., above) to the +62 BCL11a enhancer; (d) independently selected from the gRNA molecules described herein (e.g., above) to the +55 BCL11a enhancer; or (e) independently selected from the gRNA molecules described herein (e.g., above) to a HPFH region.

In an aspect, the composition includes a first gRNA molecule and a second gRNA molecule, wherein the first gRNA molecule and second gRNA molecule are complementary to different target sequences, and:

(a) the first gRNA molecule is selected from the gRNA molecules described herein (e.g., above) to the BCL11a gene, and the second gRNA molecule is selected from the gRNA molecules described herein (e.g., above) to the +58 BCL11a enhancer; (b) the first gRNA molecule is selected from the gRNA molecules described herein (e.g., above) to the BCL11a gene, and the second gRNA molecule is selected from the gRNA molecules described herein (e.g., above) to the +62 BCL11a enhancer; (c) the first gRNA molecule is selected from the gRNA molecules described herein (e.g., above) to the BCL11a gene, and the second gRNA molecule is selected from the gRNA molecules described herein (e.g., above) to the +55 BCL11a enhancer; (d) the first gRNA molecule is selected from the gRNA molecules described herein (e.g., above) to the BCL11a gene, and the second gRNA molecule is selected from the gRNA molecules described herein (e.g., above) to a HPFH region; (e) the first gRNA molecule is selected from the gRNA molecules described herein (e.g., above) to the +58 BCL11a enhancer, and the second gRNA molecule is selected from the gRNA molecules described herein (e.g., above) to the +62 BCL11a enhancer; (f) the first gRNA molecule is selected from the gRNA molecules described herein (e.g., above) to the +58 BCL11a enhancer, and the second gRNA molecule is selected from the gRNA molecules described herein (e.g., above) to the +55 BCL11a enhancer; (g) the first gRNA molecule is selected from the gRNA molecules described herein (e.g., above) to the +58 BCL11a enhancer, and the second gRNA molecule is selected from the gRNA molecules described herein (e.g., above) to a HPFH region; (h) the first gRNA molecule is selected from the gRNA molecules described herein (e.g., above) to the +62 BCL11a enhancer, and the second gRNA molecule is selected from the gRNA molecules described herein (e.g., above) to the +55 BCL11a enhancer; (i) the first gRNA molecule is selected from the gRNA molecules described herein (e.g., above) to the +62 BCL11a enhancer, and the second gRNA molecule is selected from the gRNA molecules described herein (e.g., above) to a HPFH region; (j) the first gRNA molecule is selected from the gRNA molecules described herein (e.g., above) to the +55 BCL11a enhancer, and the second gRNA molecule is selected from the gRNA molecules described herein (e.g., above) to a HPFH region;

In another aspect, the composition that includes a first gRNA molecule and a second gRNA molecule, includes:

(a) a first gRNA molecule that is selected from the gRNA molecules described herein (e.g., above) to a HPFH region, and a second gRNA molecule includes a targeting domain that is complementary to a target sequence of the beta globin gene; or (b) a first gRNA molecule that is selected from the gRNA molecules described herein (e.g., above) to a BCL11a enhancer, e.g., a +58 BCL11a enhancer, a +55 BCL11a enhancer or a +62 BCL11a enhancer, and a second gRNA molecule includes a targeting domain that is complementary to a target sequence of the beta globin gene.

In any of the aforementioned composition aspects and embodiments, the composition may consist of, with respect to the gRNA components of the composition, a first gRNA molecule and a second gRNA molecule.

In any of the aforementioned composition aspects and embodiments, the compositions may be formulated in a medium suitable for electroporation.

In another aspect, the invention provides nucleic acids encoding the gRNA molecule(s) and/or Cas molecules of the CRISPR systems. Without being bound by theory, it is believed that delivering such nucleic acids to cells will lead to the expression of the CRISPR system within the cell. In an aspect, the invention provides a nucleic acid sequence that encodes one or more gRNA molecules of any of the previous gRNA aspects and embodiments. In embodiments, the nucleic acid includes a promoter operably linked to the sequence that encodes the one or more gRNA molecules. In embodiments, the promoter is a promoter recognized by an RNA polymerase II or RNA polymerase III. In embodiments, the promoter is a U6 promoter or an HI promoter.

In further aspects, the nucleic acid further comprises sequence encoding a Cas9 molecule. In embodiments, the nucleic acid includes a promoter operably linked to the sequence that encodes a Cas9 molecule. In embodiments, the promoter is an EF-1 promoter, a CMV IE gene promoter, an EF-1α promoter, an ubiquitin C promoter, or a phosphoglycerate kinase (PGK) promoter.

In an aspect the invention provides a vector that includes the nucleic acid of any of the previous nucleic acid aspects and embodiments. In embodiments, the vector is selected from the group consisting of a lentiviral vector, an adenoviral vector, an adeno-associated viral (AAV) vector, a herpes simplex virus (HSV) vector, a plasmid, a minicircle, a nanoplasmid, and an RNA vector.

In another aspect, the invention provides a composition including one or more gRNA molecules, e.g., as described herein, e.g., in any of the previous gRNA molecule aspects and embodiments, and nucleic acid encoding a Cas9 molecule.

In another aspect, the invention provides a composition including nucleic acid encoding one or more gRNA molecules (e.g., as described herein, e.g., of any of the previous gRNA molecule aspects and embodiments), and a Cas9 molecule.

In another aspect, the invention provides a composition, e.g., a composition of any of the aforementioned composition aspects and embodiments, further including a template nucleic acid. In another aspect, the invention provides a composition, e.g., a composition of any of the aforementioned composition aspects and embodiments, further including nucleic acid sequence encoding a template nucleic acid. In embodiments, the template nucleic acid includes a nucleotide that corresponds to a nucleotide of a target sequence of the gRNA molecule. In embodiments, the template nucleic acid includes nucleic acid encoding human beta globin, e.g., human beta globin including one or more of the mutations G16D, E22A and T87Q. In embodiments, the template nucleic acid includes nucleic acid encoding human gamma globin.

In another aspect, the invention provides cells that include (or at any time included) a gRNA molecule, CRISPR system, composition or nucleic acid (e.g., as described herein, e.g., as in any of the aforementioned aspects and embodiments). In such aspects, the invention provides cells that have been modified by such inclusion.

Thus, in an aspect, the invention provides a method of altering e.g., altering the structure, e.g., sequence, of a target sequence within nucleic acid of a cell, including contacting said cell with:

1) one or more gRNA molecules of any of the aforementioned gRNA molecule aspects and embodiments, and a Cas9 molecule (e.g., as described herein); 2) one or more gRNA molecules of any of the aforementioned gRNA molecule aspects and embodiments, and nucleic acid encoding a Cas9 molecule (e.g., as described herein); 3) nucleic acid encoding one or more gRNA molecules of any of the aforementioned gRNA molecule aspects and embodiments, and a Cas9 molecule (e.g., as described herein); 4) nucleic acid encoding one or more gRNA molecules of the aforementioned gRNA molecule aspects and embodiments, and nucleic acid encoding a Cas9 molecule (e.g., as described herein); or 5) any of 1) to 4), above, and a template nucleic acid (e.g., as described herein); 6) any of 1) to 4) above, and nucleic acid including sequence encoding a template nucleic acid (e.g., as described herein); 7) a composition as described herein (e.g., of any of the aforementioned composition aspects and embodiments); or 8) the vector of any of the aforementioned vector aspects and embodiments.

In embodiments, the gRNA molecule or nucleic acid encoding the gRNA molecule, and the Cas9 molecule or nucleic acid encoding the Cas9 molecule, are formulated in a single composition. In other embodiments, the gRNA molecule or nucleic acid encoding the gRNA molecule, and the Cas9 molecule or nucleic acid encoding the Cas9 molecule, are formulated in more than one composition. In embodiments, the more than one composition are delivered simultaneously or sequentially.

In embodiments, the cell is an animal cell. In embodiments, the cell the cell is a mammalian, primate, or human cell. In embodiments, the cell is a hempatopoietic stem or progenitor cell (HSPC) (e.g., a population of HSPCs). In embodiments, the cell is a CD34+ cell. In embodiments, the cell is a CD34+/CD38−/CD90+/CD45RA− cell. In embodiments, the cell is a CD34+/CD90+/CD49f+ cell. In embodiments, the cell is a CD34+/CD38−/CD90+/CD45RA−/CD49f+ cell. In embodiments, the method includes a population of cells that has been enriched for HSPCs, e.g., for CD34+ cells.

In embodiments, the cell (e.g. population of cells) has been isolated from bone marrow. In embodiments, the cell (e.g. population of cells) has been isolated from mobilized peripheral blood. In embodiments, the cell (e.g. population of cells) has been isolated from umbilical cord blood.

In embodiments, the cell (e.g. population of cells) is autologous with respect to a patient to be administered said cell (e.g. population of cells). In embodiments, the cell (e.g. population of cells) is allogeneic with respect to a patient to be administered said cell (e.g. population of cells).

In embodiments, of the methods described herein, the altering results in an increase of fetal hemoglobin expression in the cell. In embodiments, of the methods described herein, the altering results in a reduction of fetal hemoglobin expression in the cell.

In another aspect, the invention provides a cell, altered by the method of any of the aforementioned method aspects and embodiments. In another aspect, the invention provides a cell, including a first gRNA molecule (e.g., as described herein), or a composition (e.g., as described herein), or a nucleic acid encoding the first gRNA molecule (e.g., as described herein), of any of the previous aspects and embodiments. In embodiments, the cell is an animal cell. In embodiments, the cell the cell is a mammalian, primate, or human cell. In embodiments, the cell is a hematopoietic stem or progenitor cell (HSPC) (e.g., a population of HSPCs). In embodiments, the cell is a CD34+ cell. In embodiments, the cell is a CD34+/CD38−/CD90+/CD45RA− cell. In embodiments, the cell is a CD34+/CD90+/CD49f+ cell. In embodiments, the method includes a population of cells that has been enriched for HSPCs, e.g., for CD34+ cells.

In embodiments, the cell (e.g. population of cells) has been isolated from bone marrow. In embodiments, the cell (e.g. population of cells) has been isolated from mobilized peripheral blood. In embodiments, the cell (e.g. population of cells) has been isolated from umbilical cord blood.

In embodiments, the cell (e.g. population of cells) is autologous with respect to a patient to be administered said cell (e.g. population of cells). In embodiments, the cell (e.g. population of cells) is allogeneic with respect to a patient to be administered said cell (e.g. population of cells).

In embodiments, the cell includes, has included, or will include a second gRNA molecule, e.g., as described herein, e.g., of any of the previous gRNA molecule aspects and embodiments, or a nucleic acid encoding the second gRNA molecule, wherein the first gRNA molecule and second gRNA molecule include nonidentical targeting domains.

In embodiments, expression of fetal hemoglobin is increased in the cell, e.g., relative to a cell of the same cell type that has not been modified to include a gRNA molecule (e.g., as described herein). In embodiments, expression of beta globin is decreased in the cell, e.g., relative to a cell of the same cell type that has not been modified to include a gRNA molecule (e.g., as described herein). In embodiments, expression of fetal hemoglobin is increased and expression of beta globin is decreased in the cell, e.g., relative to a cell of the same cell type that has not been modified to include a gRNA molecule (e.g., as described herein).

In an aspect, the cells of the invention (or methods comprising a cell) have been contacted with a stem cell expander, e.g., as described herein, e.g., compound 1, compound 2, compound 3 or compound 4. In an aspect, the cells of the invention (or methods comprising a cell) have been contacted with a stem cell expander, e.g., as described herein, e.g., compound 1, compound 2, compound 3, compound 4 or a combination thereof (e.g., compound 1 and compound 4). In an embodiment, the stem cell expander is compound 4. In an embodiment, the stem cell expander is a combination of compound 1 and compound 4. In embodiments, the contacting is ex vivo.

In another aspect, the invention provides methods of treatment, e.g., methods of treatment of hemoglobinopathies. In an aspect, the invention provides a method of treating a hemoglobinopathy, that includes administering to a patient a cell (e.g., a population of cells) of any of the previous cell or method aspects and embodiments.

In another aspect, the invention provides a method of increasing fetal hemoglobin expression in a mammal, including administering to a patient a cell of any of the previous cell or method aspects and embodiments. In an embodiment, the hemoglobinopathy is beta-thalassemia or sickle cell disease.

In another aspect, the invention provides a guide RNA molecule, e.g., as described herein, for use as a medicament, e.g., for use in the treatment of a disease. In embodiments, the disease is a hemoglobinopathy, e.g., beta-thalassemia or sickle cell disease.

In another aspect, the invention provides a gRNA molecule, e.g., as described herein, e.g., as described in any of the aforementioned gRNA molecule aspects and embodiments, wherein when a CRISPR system including the gRNA is introduced into a cell (e.g., a CD34+ cell, e.g., an HSC), at least about 15% of the indels produced include (a) a frameshift mutation; or (b) a large deletion, relative to unmodified target DNA, as measured by NGS. In embodiments, at least about 25% of the indels produced include (a) a frameshift mutation; or (b) a large deletion, relative to unmodified target DNA, as measured by NGS. In embodiments, at least about 40%, at least about 50%, at least about 60%, at least about 70% at least about 80%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% of the indels produced include (a) a frameshift mutation; or (b) a large deletion, relative to unmodified target DNA, as measured by NGS.

In another aspect, the invention provides methods for the ex vivo expansion and modification of HSPCs (e.g., CD34+ cells). In an aspect, the invention provides a method of modifying cells (e.g., a population of cells) including:

(a) providing a population of cells; (b) expanding said cells ex vivo in the presence of a stem cell expander; and (c) introducing into said cells a first gRNA molecule (e.g., as described herein, e.g., of any of the aforementioned gRNA molecule aspects and embodiments), a nucleic acid molecule encoding the first gRNA molecule, or a composition (e.g., as described herein, e.g., of any of the aforementioned composition aspects and embodiments); such that hemoglobin, e.g., fetal hemoglobin, expression is increased in said cells relative to the same cell type which have not been subjected to step (c).

In embodiments, the cells are introduced into a subject in need thereof, e.g., a subject that has a hemoglobinopathy, e.g., sickle cell disease or beta thalassemia.

In embodiments, the cells are or comprise CD34+ cells. In embodiments, the cells are or comprise HSPCs. In embodiments, the cells are isolated from bone marrow, mobilized peripheral blood or umbilical cord blood. In a preferred embodiment, the cells are isolated from bone marrow. In other embodiments, the cells are isolated from mobilized peripheral blood. In aspects, the moblized peripheral blood is isolated from a subject who has been administered a G-CSF. In aspects, the moblized peripheral blood is isolated from a subject who has been administered a moblization agent other than G-CSF, for example, Plerixafor® (AMD3100). In embodiments, the cells are an enriched population of cells.

In embodiments, the stem cell expander is compound 1, compound 2, compound 3, or compound 4, e.g., compound 4. In embodiments, the stem cell expander is compound 1, compound 2, compound 3, compound 4, or a combination thereof (e.g., a combination of compound 1 and compound 4). In embodiments, the cells are contacted with compound 4 at a concentration of from about 1 to about 200 micromolar (uM). In an embodiment, the concentration of compound 4 is about 75 micromolar (uM). In embodiments, the expanding said cells ex vivo in the presence of a stem cell expander occurs for a period of about 1-10 days, e.g., about 1-5 days, e.g., about 2-5 days, e.g., about 4 days.

In embodiments, the cells are autologous to a patient intended to be administered said cells. In embodiments, the cells are allogeneic to a patient intended to be administered said cells.

In embodiments, the expanding of step (b) is further in the presence of thrombopoietin (Tpo), Flt3 ligand (Flt-3L), human stem cell factor (SCF) and human interleukin-6 (IL-6). In embodiments, the thrombopoietin (Tpo), Flt3 ligand (Flt-3L), human stem cell factor (SCF) and human interleukin-6 (IL-6) are each at a concentration of about 50 ng/mL. In embodiments, the thrombopoietin (Tpo), Flt3 ligand (Flt-3L), human stem cell factor (SCF) and human interleukin-6 (IL-6) are each at a concentration of 50 ng/mL.

Additional aspects and embodiments are described below.

In an aspect, the invention provides a gRNA molecule that includes a tracr and crRNA, wherein the crRNA includes a targeting domain that is complementary with a target sequence of a BCL11A gene (e.g., a human BCL11a gene), a BCL11a enhancer (e.g., a human BCL11a enhancer), or a HFPH region (e.g., a human HPFH region).

In embodiments, the target sequence is of the BCL11A gene, and the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 1 to SEQ ID NO: 85 or SEQ ID NO: 400 to SEQ ID NO: 1231. These embodiments are referred to herein as gRNA molecule embodiment 2.

In other embodiments, the target sequence is of a BCL11a enhancer, and the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 1232 to SEQ ID NO: 1499. These embodiments are referred to herein as gRNA molecule embodiment 3. In preferred embodiments, the target sequence is of a BCL enhancer, and the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 182 to SEQ ID NO: 277 or SEQ ID NO: 334 to SEQ ID NO: 341. These embodiments are referred to herein as gRNA molecule embodiment 4. In more preferred embodiments, the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 341, SEQ ID NO: 246, SEQ ID NO: 248, SEQ ID NO: 247, SEQ ID NO: 245, SEQ ID NO: 249, SEQ ID NO: 244, SEQ ID NO: 199, SEQ ID NO: 251, SEQ ID NO: 250, SEQ ID NO: 334, SEQ ID NO: 185, SEQ ID NO: 186, SEQ ID NO: 336, or SEQ ID NO: 337. These embodiments are referred to herein as gRNA molecule embodiment 5. In still more preferred embodiments, the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 247, SEQ ID NO: 248, SEQ ID NO: 335, SEQ ID NO: 336, SEQ ID NO: 337, or SEQ ID NO: 338 (referred to herein as gRNA molecule embodiment 6), for example, includes, e.g., consists of, any one of SEQ ID NO: 248 or SEQ ID NO: 338 (referred to herein as gRNA molecule embodiment 7). In embodiments, the targeting domain includes, e.g., consists of, SEQ ID NO: 248 (referred to herein as gRNA molecule embodiment 8). In embodiments, the targeting domain includes, e.g., consists of, SEQ ID NO: 338 (referred to herein as gRNA molecule embodiment 9).

In other embodiments, the target sequence is of a BCL11a enhancer, and the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 278 to SEQ ID NO: 333 (referred to herein as gRNA molecule embodiment 10). In preferred embodiments, the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 318, SEQ ID NO: 312, SEQ ID NO: 313, SEQ ID NO: 294, SEQ ID NO: 310, SEQ ID NO: 319, SEQ ID NO: 298, SEQ ID NO: 322, SEQ ID NO: 311, SEQ ID NO: 315, SEQ ID NO: 290, SEQ ID NO: 317, SEQ ID NO: 309, SEQ ID NO: 289, or SEQ ID NO: 281 (referred to herein as gRNA molecule embodiment 11). In one preferred embodiment, the targeting domain includes, e.g., consists of, SEQ ID NO: 318 (referred to herein as gRNA molecule embodiment 12).

In other embodiments, the target sequence is of a BCL11a enhancer, and the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 1596 to SEQ ID NO: 1691 (referred to herein as gRNA molecule embodiment 13). In preferred embodiments, the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 1683, SEQ ID NO: 1638, SEQ ID NO: 1647, SEQ ID NO: 1609, SEQ ID NO: 1621, SEQ ID NO: 1617, SEQ ID NO: 1654, SEQ ID NO: 1631, SEQ ID NO: 1620, SEQ ID NO: 1637, SEQ ID NO: 1612, SEQ ID NO: 1656, SEQ ID NO: 1619, SEQ ID NO: 1675, SEQ ID NO: 1645, SEQ ID NO: 1598, SEQ ID NO: 1599, SEQ ID NO: 1663, SEQ ID NO: 1677, or SEQ ID NO: 1626 (referred to herein as gRNA molecule embodiment 14).

In other embodiments, the target sequence is of a HFPH region (e.g., a French HPFH region), and the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 86 to SEQ ID NO: 181, SEQ ID NO: 1500 to SEQ ID NO: 1595, or SEQ ID NO: 1692 to SEQ ID NO: 1761 (referred to herein as gRNA molecule embodiment 15). In preferred embodiments, the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 100, SEQ ID NO: 165, SEQ ID NO: 113, SEQ ID NO: 99, SEQ ID NO: 112, SEQ ID NO: 98, SEQ ID NO: 1580, SEQ ID NO: 106, SEQ ID NO: 1503, SEQ ID NO: 1589, SEQ ID NO: 160, SEQ ID NO: 1537, SEQ ID NO: 159, SEQ ID NO: 101, SEQ ID NO: 162, SEQ ID NO: 104, SEQ ID NO: 138, SEQ ID NO: 1536, SEQ ID NO: 1539, SEQ ID NO: 1585 (referred to herein as gRNA molecule embodiment 16). In still more preferred embodiments, the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 98, SEQ ID NO: 100, SEQ ID NO: 1505, SEQ ID NO: 1589, SEQ ID NO: 1700, or SEQ ID NO: 1750 (referred to herein as gRNA molecule embodiment 17). In other preferred embodiments, the targeting domain includes, e.g., consists of, any one of SEQ ID NO: 100, SEQ ID NO: 165, or SEQ ID NO: 113 (referred to herein as gRNA molecule embodiment 18).

In embodiments, the gRNA molecule includes a targeting domain that includes, e.g., consists of, 17, 18, 19, 20, 21, 22, 23, or 24, preferably 20, consecutive nucleic acids of any targeting domain sequence described herein, for example a targeting domain sequence of Table 1 or Table 2. In embodiments, the 17, 18, 19, 20, 21, 22, 23, or 24, preferably 20, consecutive nucleic acids of any one of targeting domain sequences described herein, for example a targeting domain sequence of Table 1 or Table 2, are the 17, 18, 19, 20, 21, 22, 23, or 24, preferably 20, consecutive nucleic acids disposed at the 3′ end of the recited targeting domain sequence. In other embodiments, the 17, 18, 19, 20, 21, 22, 23, or 24, preferably 20, consecutive nucleic acids of any one of the targeting domain sequences described herein, for example a targeting domain sequence of Table 1 or Table 2, are the 17, 18, 19, 20, 21, 22, 23, or 24, preferably 20, consecutive nucleic acids disposed at the 5′ end of the recited targeting domain sequence. In other embodiments, the 17, 18, 19, 20, 21, 22, 23, or 24, preferably 20, consecutive nucleic acids of any one of the targeting domain sequences described herein, for example a targeting domain sequence of Table 1 or Table 2, do not include either the 5′ or 3′ nucleic acid of the recited targeting domain sequence.

In embodiments, the gRNA molecule includes a targeting domain that includes, e.g., consists of, 17, 18, 19, or 20, preferably 20, consecutive nucleic acids of any targeting domain sequence described herein, for example a targeting domain sequence of Table 5, Table 6, Table 7, Table 8 or Table 9. In embodiments, the 17, 18, 19, or 20, preferably 20, consecutive nucleic acids of any one of targeting domain sequences described herein, for example a targeting domain sequence of Table 5, Table 6, Table 7, Table 8 or Table 9, are the 17, 18, 19, or 20, preferably 20, consecutive nucleic acids disposed at the 3′ end of the recited targeting domain sequence. In other embodiments, the 17, 18, 19, or 20, preferably 20, consecutive nucleic acids of any one of the targeting domain sequences described herein, for example a targeting domain sequence of Table 5, Table 6, Table 7, Table 8 or Table 9, are the 17, 18, 19, or 20, preferably 20, consecutive nucleic acids disposed at the 5′ end of the recited targeting domain sequence. In other embodiments, the 17, 18, 19, or 20, preferably 20, consecutive nucleic acids of any one of the targeting domain sequences described herein, for example a targeting domain sequence of Table 5, Table 6, Table 7, Table 8 or Table 9, do not include either the 5′ or 3′ nucleic acid of the recited targeting domain sequence.

The following aspects describe features of the gRNA molecule that may be combined with any of the aforementioned aspects and embodiments. In embodiments, the gRNA molecule, including the gRNA molecule of any of the aforementioned aspects and embodiments, include a portion of the crRNA and a portion of the tracr that hybridize to form a flagpole that includes SEQ ID NO: 6584 or 6585. In embodiments, the flagpole further includes a first flagpole extension, located 3′ to the crRNA portion of the flagpole, wherein said first flagpole extension includes SEQ ID NO: 6586. In embodiments, the flagpole further includes (in addition to or in alternative to the first flagpole extension) a second flagpole extension located 3′ to the crRNA portion of the flagpole and, if present, the first flagpole extension, wherein said second flagpole extension includes SEQ ID NO: 6587.

In embodiments, including in any of the aforementioned aspects and embodiments, the tracr includes SEQ ID NO: 6660 or SEQ ID NO: 6661. In embodiments, the tracr includes SEQ ID NO: 7812, optionally further including, at the 3′ end, an additional 1, 2, 3, 4, 5, 6, or 7 uracil (U) nucleotides. In embodiments, the crRNA includes, from 5′ to 3′, [targeting domain]-: a) SEQ ID NO: 6584; b) SEQ ID NO: 6585; c) SEQ ID NO: 6605; d) SEQ ID NO: 6606; e) SEQ ID NO: 6607; f) SEQ ID NO: 6608; or g) SEQ ID NO: 7806.

In embodiments, including in any of the aforementioned aspects and embodiments, the tracr includes, from 5′ to 3′: a) SEQ ID NO: 6589; b) SEQ ID NO: 6590; c) SEQ ID NO: 6609; d) SEQ ID NO: 6610; e) SEQ ID NO: 6660; f) SEQ ID NO: 6661; g) SEQ ID NO: 7812; h) SEQ ID NO: 7807; i) SEQ ID NO: 7808; j) SEQ ID NO: 7809; k) any of a) to j), above, further including, at the 3′ end, at least 1, 2, 3, 4, 5, 6 or 7 uracil (U) nucleotides, e.g., 1, 2, 3, 4, 5, 6, or 7 uracil (U) nucleotides; 1) any of a) to k), above, further including, at the 3′ end, at least 1, 2, 3, 4, 5, 6 or 7 adenine (A) nucleotides, e.g., 1, 2, 3, 4, 5, 6, or 7 adenine (A) nucleotides; or m) any of a) to l), above, further including, at the 5′ end (e.g., at the 5′ terminus), at least 1, 2, 3, 4, 5, 6 or 7 adenine (A) nucleotides, e.g., 1, 2, 3, 4, 5, 6, or 7 adenine (A) nucleotides.

In embodiments, the targeting domain and the tracr are disposed on separate nucleic acids molecules. In embodiments of such gRNA molecules, the nucleic acid molecule including the targeting domain includes SEQ ID NO: 6607, optionally disposed immediately 3′ to the targeting domain, and the nucleic acid molecule including the tracr includes, e.g., consists of, SEQ ID NO: 6660.

In embodiments, the crRNA portion of the flagpole includes SEQ ID NO: 6607 or SEQ ID NO: 6608.

In embodiments, the tracr includes SEQ ID NO: 6589 or 6590, and optionally, if a first flagpole extension is present, a first tracr extension, disposed 5′ to SEQ ID NO: 6589 or 6590, said first tracr extension including SEQ ID NO: 6591.

In embodiments, including in embodiments of any of the aforementioned aspects and embodiments, the targeting domain and the tracr are disposed on separate nucleic acid molecules. In other embodiments, including in embodiments of any of the aforementioned aspects and embodiments, the targeting domain and the tracr are disposed on a single nucleic acid molecule, for example, the tracr is disposed 3′ to the targeting domain.

In embodiments, when the targeting domain and the tracr are disposed on a single nucleic acid molecule, the gRNA molecule further includes a loop, disposed 3′ to the targeting domain and 5′ to the tracr. In embodiments, the loop includes, e.g., consists of, SEQ ID NO: 6588.

In embodiments, when the targeting domain and the tracr are disposed on a single nucleic acid molecule, the gRNA molecule includes, from 5′ to 3′, [targeting domain]-: (a) SEQ ID NO: 6601; (b) SEQ ID NO: 6602; (c) SEQ ID NO: 6603; (d) SEQ ID NO: 6604; (e) SEQ ID NO: 7811; or (f) any of (a) to (e), above, further including, at the 3′ end, 1, 2, 3, 4, 5, 6 or 7 uracil (U) nucleotides. In embodiments, the gRNA molecule includes, e.g., consists of, said targeting domain and SEQ ID NO: 7811, optionally disposed immediately 3′ to said targeting domain.

In embodiments, including in any of the aforementioned aspects and embodiments, each of the nucleic acid residues of the gRNA molecule is an unmodified A, U, G or C nucleic acid residue and unmodified phosphate bonds between each residue of the nucleic acid molecule(s). In other embodiments, including in any of the aforementioned aspects and embodiments, one, or optionally more than one, of the nucleic acid molecules that make up the gRNA molecule includes: a) one or more, e.g., three, phosphorothioate modifications at the 3′ end of said nucleic acid molecule or molecules; b) one or more, e.g., three, phosphorothioate modifications at the 5′ end of said nucleic acid molecule or molecules; c) one or more, e.g., three, 2′-O-methyl modifications at the 3′ end of said nucleic acid molecule or molecules; d) one or more, e.g., three, 2′-O-methyl modifications at the 5′ end of said nucleic acid molecule or molecules; e) a 2′ O-methyl modification at each of the 4^(th)-to-terminal, 3^(rd)-to-terminal, and 2^(nd)-to-terminal 3′ residues of said nucleic acid molecule or molecules; f) a 2′ O-methyl modification at each of the 4^(th)-to-terminal, 3^(rd)-to-terminal, and 2^(nd)-to-terminal 5′ residues of said nucleic acid molecule or molecules; or f) any combination thereof.

In preferred embodiments, the invention provides a gRNA molecule (e.g., that is a sgRNA molecule) including, e.g., consisting of, the sequence: (a) SEQ ID NO: 342; (b) SEQ ID NO: 343; or (c) SEQ ID NO: 1762 (referred to in this summary of invention as gRNA molecule embodiment 41).

In other preferred embodiments, the invention provides gRNA molecule (e.g., that is a dual gRNA molecule) including, e.g., consisting of: (a) a crRNA including, e.g., consisting of, SEQ ID NO: 344, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA including, e.g., consisting of, SEQ ID NO: 344, and a tracr including, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA including, e.g., consisting of, SEQ ID NO: 345, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA including, e.g., consisting of, SEQ ID NO: 345, and a tracr including, e.g., consisting of, SEQ ID NO: 346 (referred to in this summary of invention as gRNA molecule embodiment 42).

In other preferred embodiments, the invention provides a gRNA molecule (e.g., that is a sgRNA molecule) including, e.g., consisting of, the sequence: (a) SEQ ID NO: 347; (b) SEQ ID NO: 348; or (c) SEQ ID NO: 1763 (referred to in this summary of invention as gRNA molecule embodiment 43).

In other preferred embodiments, the invention provides gRNA molecule (e.g., that is a dual gRNA molecule) including, e.g., consisting of: (a) a crRNA including, e.g., consisting of, SEQ ID NO: 349, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA including, e.g., consisting of, SEQ ID NO: 349, and a tracr including, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA including, e.g., consisting of, SEQ ID NO: 350, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA including, e.g., consisting of, SEQ ID NO: 350, and a tracr including, e.g., consisting of, SEQ ID NO: 346 (referred to in this summary of invention as gRNA molecule embodiment 44).

In other preferred embodiments, the invention provides a gRNA molecule (e.g., that is a sgRNA molecule) including, e.g., consisting of, the sequence: (a) SEQ ID NO: 351; (b) SEQ ID NO: 352; or (c) SEQ ID NO: 1764 (referred to in this summary of invention as gRNA molecule embodiment 45).

In other preferred embodiments, the invention provides gRNA molecule (e.g., that is a dual gRNA molecule) including, e.g., consisting of: (a) a crRNA including, e.g., consisting of, SEQ ID NO: 353, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA including, e.g., consisting of, SEQ ID NO: 353, and a tracr including, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA including, e.g., consisting of, SEQ ID NO: 354, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA including, e.g., consisting of, SEQ ID NO: 354, and a tracr including, e.g., consisting of, SEQ ID NO: 346 (referred to in this summary of invention as gRNA molecule embodiment 46).

In other preferred embodiments, the invention provides a gRNA molecule (e.g., that is a sgRNA molecule) including, e.g., consisting of, the sequence: (a) SEQ ID NO: 355; (b) SEQ ID NO: 356; or (c) SEQ ID NO: 1765 (referred to in this summary of invention as gRNA molecule embodiment 47).

In other preferred embodiments, the invention provides gRNA molecule (e.g., that is a dual gRNA molecule) including, e.g., consisting of: (a) a crRNA including, e.g., consisting of, SEQ ID NO: 357, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA including, e.g., consisting of, SEQ ID NO: 357, and a tracr including, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA including, e.g., consisting of, SEQ ID NO: 358, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA including, e.g., consisting of, SEQ ID NO: 358, and a tracr including, e.g., consisting of, SEQ ID NO: 346 (referred to in this summary of invention as gRNA molecule embodiment 48).

In other preferred embodiments, the invention provides a gRNA molecule (e.g., that is a sgRNA molecule) including, e.g., consisting of, the sequence: (a) SEQ ID NO: 359; (b) SEQ ID NO: 360; or (c) SEQ ID NO: 1766 (referred to in this summary of invention as gRNA molecule embodiment 49).

In other preferred embodiments, the invention provides gRNA molecule (e.g., that is a dual gRNA molecule) including, e.g., consisting of: (a) a crRNA including, e.g., consisting of, SEQ ID NO: 361, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA including, e.g., consisting of, SEQ ID NO: 361, and a tracr including, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA including, e.g., consisting of, SEQ ID NO: 362, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA including, e.g., consisting of, SEQ ID NO: 362, and a tracr including, e.g., consisting of, SEQ ID NO: 346 (referred to in this summary of invention as gRNA molecule embodiment 50).

In other preferred embodiments, the invention provides a gRNA molecule (e.g., that is a sgRNA molecule) including, e.g., consisting of, the sequence: (a) SEQ ID NO: 363; (b) SEQ ID NO: 364; or (c) SEQ ID NO: 1767 (referred to in this summary of invention as gRNA molecule embodiment 51).

In other preferred embodiments, the invention provides gRNA molecule (e.g., that is a dual gRNA molecule) including, e.g., consisting of: (a) a crRNA including, e.g., consisting of, SEQ ID NO: 365, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA including, e.g., consisting of, SEQ ID NO: 365, and a tracr including, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA including, e.g., consisting of, SEQ ID NO: 366, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA including, e.g., consisting of, SEQ ID NO: 366, and a tracr including, e.g., consisting of, SEQ ID NO: 346 (referred to in this summary of invention as gRNA molecule embodiment 52).

In other preferred embodiments, the invention provides a gRNA molecule (e.g., that is a sgRNA molecule) including, e.g., consisting of, the sequence: (a) SEQ ID NO: 367; (b) SEQ ID NO: 368; or (c) SEQ ID NO: 1768 (referred to in this summary of invention as gRNA molecule embodiment 53).

In other preferred embodiments, the invention provides gRNA molecule (e.g., that is a dual gRNA molecule) including, e.g., consisting of: (a) a crRNA including, e.g., consisting of, SEQ ID NO: 369, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA including, e.g., consisting of, SEQ ID NO: 369, and a tracr including, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA including, e.g., consisting of, SEQ ID NO: 370, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA including, e.g., consisting of, SEQ ID NO: 370, and a tracr including, e.g., consisting of, SEQ ID NO: 346 (referred to in this summary of invention as gRNA molecule embodiment 54).

In other preferred embodiments, the invention provides a gRNA molecule (e.g., that is a sgRNA molecule) including, e.g., consisting of, the sequence: (a) SEQ ID NO: 371; (b) SEQ ID NO: 372; or (c) SEQ ID NO: 1769 (referred to in this summary of invention as gRNA molecule embodiment 55).

In other preferred embodiments, the invention provides gRNA molecule (e.g., that is a dual gRNA molecule) including, e.g., consisting of: (a) a crRNA including, e.g., consisting of, SEQ ID NO: 373, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA including, e.g., consisting of, SEQ ID NO: 373, and a tracr including, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA including, e.g., consisting of, SEQ ID NO: 374, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA including, e.g., consisting of, SEQ ID NO: 374, and a tracr including, e.g., consisting of, SEQ ID NO: 346 (referred to in this summary of invention as gRNA molecule embodiment 56).

In other preferred embodiments, the invention provides a gRNA molecule (e.g., that is a sgRNA molecule) including, e.g., consisting of, the sequence: (a) SEQ ID NO: 375; (b) SEQ ID NO: 376; or (c) SEQ ID NO: 1770 (referred to in this summary of invention as gRNA molecule embodiment 57).

In other preferred embodiments, the invention provides gRNA molecule (e.g., that is a dual gRNA molecule) including, e.g., consisting of: (a) a crRNA including, e.g., consisting of, SEQ ID NO: 377, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA including, e.g., consisting of, SEQ ID NO: 377, and a tracr including, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA including, e.g., consisting of, SEQ ID NO: 378, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA including, e.g., consisting of, SEQ ID NO: 378, and a tracr including, e.g., consisting of, SEQ ID NO: 346 (referred to in this summary of invention as gRNA molecule embodiment 58).

In other preferred embodiments, the invention provides a gRNA molecule (e.g., that is a sgRNA molecule) including, e.g., consisting of, the sequence: (a) SEQ ID NO: 379; (b) SEQ ID NO: 380; or (c) SEQ ID NO: 1771 (referred to in this summary of invention as gRNA molecule embodiment 59).

In other preferred embodiments, the invention provides gRNA molecule (e.g., that is a dual gRNA molecule) including, e.g., consisting of: (a) a crRNA including, e.g., consisting of, SEQ ID NO: 381, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA including, e.g., consisting of, SEQ ID NO: 381, and a tracr including, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA including, e.g., consisting of, SEQ ID NO: 382, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA including, e.g., consisting of, SEQ ID NO: 382, and a tracr including, e.g., consisting of, SEQ ID NO: 346 (referred to in this summary of invention as gRNA molecule embodiment 60).

In other preferred embodiments, the invention provides a gRNA molecule (e.g., that is a sgRNA molecule) including, e.g., consisting of, the sequence: (a) SEQ ID NO: 383; (b) SEQ ID NO: 384; or (c) SEQ ID NO: 1772 (referred to in this summary of invention as gRNA molecule embodiment 61).

In other preferred embodiments, the invention provides gRNA molecule (e.g., that is a dual gRNA molecule) including, e.g., consisting of: (a) a crRNA including, e.g., consisting of, SEQ ID NO: 385, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA including, e.g., consisting of, SEQ ID NO: 385, and a tracr including, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA including, e.g., consisting of, SEQ ID NO: 386, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA including, e.g., consisting of, SEQ ID NO: 386, and a tracr including, e.g., consisting of, SEQ ID NO: 346 (referred to in this summary of invention as gRNA molecule embodiment 62).

In other preferred embodiments, the invention provides a gRNA molecule (e.g., that is a sgRNA molecule) including, e.g., consisting of, the sequence: (a) SEQ ID NO: 387; (b) SEQ ID NO: 388; or (c) SEQ ID NO: 1773 (referred to in this summary of invention as gRNA molecule embodiment 63).

In other preferred embodiments, the invention provides gRNA molecule (e.g., that is a dual gRNA molecule) including, e.g., consisting of: (a) a crRNA including, e.g., consisting of, SEQ ID NO: 389, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA including, e.g., consisting of, SEQ ID NO: 389, and a tracr including, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA including, e.g., consisting of, SEQ ID NO: 390, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA including, e.g., consisting of, SEQ ID NO: 390, and a tracr including, e.g., consisting of, SEQ ID NO: 346 (referred to in this summary of invention as gRNA molecule embodiment 64).

In other preferred embodiments, the invention provides a gRNA molecule (e.g., that is a sgRNA molecule) including, e.g., consisting of, the sequence: (a) SEQ ID NO: 391; (b) SEQ ID NO: 392; or (c) SEQ ID NO: 1774 (referred to in this summary of invention as gRNA molecule embodiment 65).

In other preferred embodiments, the invention provides gRNA molecule (e.g., that is a dual gRNA molecule) including, e.g., consisting of: (a) a crRNA including, e.g., consisting of, SEQ ID NO: 393, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA including, e.g., consisting of, SEQ ID NO: 393, and a tracr including, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA including, e.g., consisting of, SEQ ID NO: 394, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA including, e.g., consisting of, SEQ ID NO: 394, and a tracr including, e.g., consisting of, SEQ ID NO: 346 (referred to in this summary of invention as gRNA molecule embodiment 66).

In other preferred embodiments, the invention provides a gRNA molecule (e.g., that is a sgRNA molecule) including, e.g., consisting of, the sequence: (a) SEQ ID NO: 395; (b) SEQ ID NO: 396; or (c) SEQ ID NO: 1775 (referred to in this summary of invention as gRNA molecule embodiment 67).

In other preferred embodiments, the invention provides gRNA molecule (e.g., that is a dual gRNA molecule) including, e.g., consisting of: (a) a crRNA including, e.g., consisting of, SEQ ID NO: 397, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA including, e.g., consisting of, SEQ ID NO: 397, and a tracr including, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA including, e.g., consisting of, SEQ ID NO: 398, and a tracr including, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA including, e.g., consisting of, SEQ ID NO: 398, and a tracr including, e.g., consisting of, SEQ ID NO: 346 (referred to in this summary of invention as gRNA molecule embodiment 68).

In embodiments, including in any of the aforementioned aspects and embodiments, the invention provides a gRNA molecule, wherein when a CRISPR system (e.g., an RNP as described herein) including the gRNA molecule is introduced into a cell, an indel is formed at or near the target sequence complementary to the targeting domain of the gRNA molecule. In embodiments, including in embodiments comprising a targeting domain complementary to a target sequence of a +58 Enhancer region, the indel does not include a nucleotide of a GATA-1 and/or TAL-1 binding site. In embodiments, the indel does not interfere with the binding of GATA-1 and/or TAL-1 to their binding sites. In embodiments, including in any of the aforementioned aspects and embodiments, the invention provides a gRNA molecule, wherein when a CRISPR system (e.g., an RNP as described herein) including the gRNA molecule is introduced into a population of cells, an indel is formed at or near the target sequence complementary to the targeting domain of the gRNA molecule in at least about 40%, e.g., at least about 50%, e.g., at least about 60%, e.g., at least about 70%, e.g., at least about 80%, e.g., at least about 90%, e.g., at least about 95%, e.g., at least about 96%, e.g., at least about 97%, e.g., at least about 98%, e.g., at least about 99%, of the cells of the population. In embodiments, including in any of the aforementioned aspects and embodiments, the invention provides a gRNA molecule, wherein when a CRISPR system (e.g., an RNP as described herein) including the gRNA molecule is introduced into a population of cells, an indel that does not include a nucleotide of a GATA-1 and/or TAL-1 binding site is formed at or near the target sequence complementary to the targeting domain of the gRNA molecule in at least about 20%, e.g., at least about 30%, e.g., at least about 35%, e.g., at least about 40%, e.g., at least about 45%, e.g., at least about 50%, e.g., at least about 55%, e.g., at least about 60%, e.g., at least about 65%, e.g., at least about 70%, e.g., at least about 75%, e.g., at least about 80%, e.g., at least about 85%, e.g., at least about 90%, e.g., at least about 95%, e.g., at least about 99%, of the cells of the population. In embodiments, including in any of the aforementioned aspects and embodiments, the indel is an indel listed in any of FIG. 25, Table 15, Table 26, Table 27 or Table 37. In embodiments, in at least about 30%, e.g., least about 40%, e.g., at least about 50%, e.g., at least about 60%, e.g., at least about 70%, e.g., at least about 80%, e.g., at least about 90%, e.g., at least about 95%, e.g., at least about 96%, e.g., at least about 97%, e.g., at least about 98%, e.g., at least about 99%, of the cells of the population, the indel is an indel listed in any of FIG. 25, Table 15, Table 26, Table 27 or Table 37. In embodiments, the three most frequently detected indels in said population of cells include the indels associated with any gRNA molecule listed in any of FIG. 25, Table 15, Table 26, Table 27 or Table 37. In embodiments, the indel (or pattern of top indels) is as measured by next generation sequencing (NGS), e.g., as described in the art. In embodiments, including in any of the aforementioned aspects and embodiments, the invention provides a gRNA molecule, wherein when a CRISPR system (e.g., an RNP as described herein) including the gRNA molecule is introduced into a cell, no off-target indels are formed in said cell, e.g., as detectible by next generation sequencing and/or a nucleotide insertional assay, e.g., assayed in an HPCS cell, e.g., a CD34+ cell. In embodiments, including in any of the aforementioned aspects and embodiments, the invention provides a gRNA molecule, wherein when a CRISPR system (e.g., an RNP as described herein) including the gRNA molecule is introduced into a population of cells, no off-target indel is detected in more than about 5%, e.g., more than about 1%, e.g., more than about 0.1%, e.g., more than about 0.01%, of the cells of the population of cells, e.g., as detectible by next generation sequencing and/or a nucleotide insertional assay, e.g., assayed in a population of HPSC cells, e.g., a population of CD34+ cells.

In embodiments, including in any of the aforementioned aspects and embodiments, the invention provides a gRNA molecule, wherein when a CRISPR system (e.g., an RNP as described herein) including the gRNA molecule is introduced into a cell, expression of fetal hemoglobin is increased in said cell or its progeny, e.g., its erythroid progeny, e.g., its red blood cell progeny. In embodiments, expression of fetal hemoglobin is increased in said cell or its progeny, e.g., its erythroid progeny, e.g., its red blood cell progeny, by at least about 20%, e.g., at least about 30%, e.g., at least about 40%, e.g., at least about 50%, e.g., at least about 60%, e.g., at least about 70%, e.g., at least about 80%, e.g., at least about 90%, e.g., at least about 95%, e.g., at least about 96%, e.g., at least about 97%, e.g., at least about 98%, e.g., at least about 99%. In embodiments, said cell or its progeny, e.g., its erythroid progeny, e.g., its red blood cell progeny, produces at least about 6 picograms (e.g., at least about 7 picograms, at least about 8 picograms, at least about 9 picograms, at least about 10 picograms, or from about 8 to about 9 picograms, or from about 9 to about 10 picograms) fetal hemoglobin per cell. In embodiments, including in any of the aforementioned aspects and embodiments, the invention provides a gRNA molecule, wherein when a CRISPR system (e.g., an RNP as described herein) including the gRNA molecule is introduced into a cell, levels of fetal hemoglobin (e.g., gamma globin) mRNA are increased in said cell or its progeny, e.g., its erythroid progeny, e.g., its red blood cell progeny. In embodiments, including in any of the aforementioned aspects and embodiments, the invention provides a gRNA molecule, wherein when a CRISPR system (e.g., an RNP as described herein) including the gRNA molecule is introduced into a cell, expression of BCL11a mRNA is decreased in said cell or its progeny, e.g., its erythroid progeny, e.g., its red blood cell progeny. In embodiments, including in any of the aforementioned aspects and embodiments, the invention provides a gRNA molecule, wherein when a CRISPR system (e.g., an RNP as described herein) including the gRNA molecule is introduced into a cell, levels of BCL11a mRNA are decreased in said cell or its progeny, e.g., its erythroid progeny, e.g., its red blood cell progeny.

In any of the aforementioned aspects and embodiments that mention a cell, the cell is (or population of cells includes) a mammalian, primate, or human cell, e.g., is a human cell or population of human cells. In embodiments, the cell is (or population of cells includes) an HSPC, for example, is CD34+, for example, is CD34+CD90+. In embodiments, the cell (or population of cells) is autologous with respect to a patient to be administered said cell. In other embodiments, the cell (or population of cells) is allogeneic with respect to a patient to be administered said cell.

In another aspect, the invention provides a composition including: 1) one or more gRNA molecules (including a first gRNA molecule) described herein, for example, one or more gRNA molecules of any of the previous aspects and embodiments, and a Cas9 molecule, for example, as described herein; 2) one or more gRNA molecules (including a first gRNA molecule) described herein, for example, one or more gRNA molecules of any of the previous aspects and embodiments, and nucleic acid encoding a Cas9 molecule (described herein); 3) nucleic acid encoding one or more gRNA molecules (including a first gRNA molecule) described herein, for example, one or more gRNA molecules of any of the previous aspects and embodiments, and a Cas9 molecule (described herein); 4) nucleic acid encoding one or more gRNA molecules (including a first gRNA molecule) described herein, for example, one or more gRNA molecules of any of the previous aspects and embodiments, and nucleic acid encoding a Cas9 molecule (described herein); or 5) any of 1) to 4), above, and a template nucleic acid; or 6) any of 1) to 4) above, and nucleic acid including sequence encoding a template nucleic acid.

In preferred embodiments, the invention provides a composition including a first gRNA molecule (e.g., described herein, e.g., a first gRNA molecule of any of the previous gRNA molecule aspects and embodiments), further including a Cas9 molecule (described herein).

In embodiments, the Cas9 molecule is an active or inactive s. pyogenes Cas9. In embodiments, the Cas9 molecule includes SEQ ID NO: 6611. In embodiments, the Cas9 molecule includes, e.g., consists of: (a) SEQ ID NO: 7821; (b) SEQ ID NO: 7822; (c) SEQ ID NO: 7823; (d) SEQ ID NO: 7824; (e) SEQ ID NO: 7825; (f) SEQ ID NO: 7826; (g) SEQ ID NO: 7827; (h) SEQ ID NO: 7828; (i) SEQ ID NO: 7829; (j) SEQ ID NO: 7830; or (k) SEQ ID NO: 7831.

In preferred embodiments, the first gRNA molecule and Cas9 molecule are present in a ribonuclear protein complex (RNP).

In embodiments, the invention provides a composition, e.g., a composition of any of the previous aspects and embodiments, further including a second gRNA molecule; a second gRNA molecule and a third gRNA molecule; or a second gRNA molecule, optionally, a third gRNA molecule, and, optionally, a fourth gRNA molecule, wherein the second gRNA molecule, the optional third gRNA molecule, and the optional fourth gRNA molecule are a gRNA molecule of a gRNA molecule described herein, e.g., a gRNA molecule of any of the previous gRNA molecule aspects and embodiments, and wherein each gRNA molecule of the composition is complementary to a different target sequence.

In embodiments, two or more of the first gRNA molecule, the second gRNA molecule, the optional third gRNA molecule, and the optional fourth gRNA molecule are complementary to target sequences within the same gene or region. In embodiments, the first gRNA molecule, the second gRNA molecule, the optional third gRNA molecule, and the optional fourth gRNA molecule are complementary to target sequences not more than 20000 nucleotides, not more than 10000 nucleotides, not more than 6000, not more than 5000 nucleotides, not more than 4000, not more than 1000 nucleotides, not more than 500 nucleotides, not more than 400 nucleotides, not more than 300 nucleotides, not more than 200 nucleotides, not more than 100 nucleotides, not more than 90 nucleotides, not more than 80 nucleotides, not more than 70 nucleotides, not more than 60 nucleotides, not more than 50 nucleotides, not more than 40 nucleotides, not more than 30 nucleotides, not more than 20 nucleotides or not more than 10 nucleotides apart.

In other embodiments, two or more of the first gRNA molecule, the second gRNA molecule, the optional third gRNA molecule, and the optional fourth gRNA molecule are complementary to target sequence within different genes or regions.

In embodiments, including in any of the aforementioned composition aspects and embodiments, the invention provides a composition including a first gRNA molecule and a second gRNA molecule, wherein the first gRNA molecule and second gRNA molecule are:

(a) independently selected from the gRNA molecules of gRNA molecule embodiment 4, and are complementary to different target sequences; (b) independently selected from the gRNA molecules of gRNA molecule embodiment 5, and are complementary to different target sequences; c) independently selected from the gRNA molecules of gRNA molecule embodiment 6, and are complementary to different target sequences; or (d) independently selected from the gRNA molecules of gRNA molecule embodiment 7, and are complementary to different target sequences; or (e) independently selected from the gRNA molecules of any of gRNA molecule embodiments 41-56, and are complementary to different target sequences.

In embodiments, including in any of the aforementioned composition aspects and embodiments, the invention provides a composition including a first gRNA molecule and a second gRNA molecule, wherein the first gRNA molecule and second gRNA molecule are:

(a) independently selected from the gRNA molecules of gRNA molecule embodiment 10, and are complementary to different target sequences; or (b) independently selected from the gRNA molecules of gRNA molecule embodiment 11, and are complementary to different target sequences.

In embodiments, including in any of the aforementioned composition aspects and embodiments, the invention provides a composition, including a first gRNA molecule and a second gRNA molecule, wherein the first gRNA molecule and second gRNA molecule are:

(a) independently selected from the gRNA molecules of gRNA molecule embodiment 13, and are complementary to different target sequences; or (b) independently selected from the gRNA molecules of gRNA molecule embodiment 14, and are complementary to different target sequences.

In embodiments, including in any of the aforementioned composition aspects and embodiments, the invention provides a composition, including a first gRNA molecule and a second gRNA molecule, wherein the first gRNA molecule and second gRNA molecule are:

(a) independently selected from the gRNA molecules of gRNA molecule embodiment 16, and are complementary to different target sequences; (b) independently selected from the gRNA molecules of gRNA molecule embodiment 17, and are complementary to different target sequences; (c) independently selected from the gRNA molecules of gRNA molecule embodiment 18, and are complementary to different target sequences; or (d) independently selected from the gRNA molecules of any of gRNA molecule embodiments 57-68, and are complementary to different target sequences.

In embodiments, including in any of the aforementioned composition aspects and embodiments, the invention provides a composition, including a first gRNA molecule and a second gRNA molecule, wherein:

(1) the first gRNA molecule is: (a) selected from the gRNA molecules of gRNA molecule embodiment 4, (b) selected from the gRNA molecules of gRNA molecule embodiment 5, (c) selected from the gRNA molecules of gRNA molecule embodiment 6, (d) selected from the gRNA molecules of gRNA molecule embodiment 7, or (e) selected from the gRNA molecules of any of gRNA molecule embodiments 41-56; and (2) the second gRNA molecule is: (a) selected from the gRNA molecules of gRNA molecule embodiment 10, or (b) selected from the gRNA molecules of gRNA molecule embodiment 11.

In embodiments, including in any of the aforementioned composition aspects and embodiments, the invention provides a composition, including a first gRNA molecule and a second gRNA molecule, wherein:

(1) the first gRNA molecule is: (a) selected from the gRNA molecules of gRNA molecule embodiment 4, (b) selected from the gRNA molecules of gRNA molecule embodiment 5, (c) selected from the gRNA molecules of gRNA molecule embodiment 6, (d) selected from the gRNA molecules of gRNA molecule embodiment 7, or (e) selected from the gRNA molecules of any of gRNA molecule embodiments 41-56; and (2) the second gRNA molecule is: (a) selected from the gRNA molecules of gRNA molecule embodiment 13, (b) selected from the gRNA molecules of gRNA molecule embodiment 14.

In embodiments, including in any of the aforementioned composition aspects and embodiments, the invention provides a composition, including a first gRNA molecule and a second gRNA molecule, wherein:

(1) the first gRNA molecule is: (a) selected from the gRNA molecules of gRNA molecule embodiment 4, (b) selected from the gRNA molecules of gRNA molecule embodiment 5, (c) selected from the gRNA molecules of gRNA molecule embodiment 6, (d) selected from the gRNA molecules of gRNA molecule embodiment 7, or (e) selected from the gRNA molecules of any of gRNA molecule embodiments 41-56; and (2) the second gRNA molecule is: (a) selected from the gRNA molecules of gRNA molecule embodiment 16, (b) selected from the gRNA molecules of gRNA molecule embodiment 17, (c) selected from the gRNA molecules of gRNA molecule embodiment 18, or (d) selected from the gRNA molecules of any of gRNA molecule embodiments 57-68.

In embodiments, including in any of the aforementioned composition aspects and embodiments, the invention provides a composition, including a first gRNA molecule and a second gRNA molecule, wherein:

(1) the first gRNA molecule is: (a) selected from the gRNA molecules of gRNA molecule embodiment 10, or (b) selected from the gRNA molecules of gRNA molecule embodiment 11; and (2) the second gRNA molecule is: (a) selected from the gRNA molecules of gRNA molecule embodiment 13, (b) selected from the gRNA molecules of gRNA molecule embodiment 14.

In embodiments, including in any of the aforementioned composition aspects and embodiments, the invention provides a composition, including a first gRNA molecule and a second gRNA molecule, wherein:

(1) the first gRNA molecule is: (a) selected from the gRNA molecules of gRNA molecule embodiment 10, or (b) selected from the gRNA molecules of gRNA molecule embodiment 11; and (2) the second gRNA molecule is: (a) selected from the gRNA molecules of gRNA molecule embodiment 16, (b) selected from the gRNA molecules of gRNA molecule embodiment 17, (c) selected from the gRNA molecules of gRNA molecule embodiment 18, or (d) selected from the gRNA molecules of any of gRNA molecule embodiments 57-68.

In embodiments, including in any of the aforementioned composition aspects and embodiments, the invention provides a composition, including a first gRNA molecule and a second gRNA molecule, wherein:

(1) the first gRNA molecule is: (a) selected from the gRNA molecules of gRNA molecule embodiment 13, (b) selected from the gRNA molecules of gRNA molecule embodiment 14; and (2) the second gRNA molecule is: (a) selected from the gRNA molecules of gRNA molecule embodiment 16, (b) selected from the gRNA molecules of gRNA molecule embodiment 17, (c) selected from the gRNA molecules of gRNA molecule embodiment 18, or (d) selected from the gRNA molecules of any of gRNA molecule embodiments 57-68.

In embodiments, including in any of the aforementioned composition aspects and embodiments, the invention provides a composition, including a first gRNA molecule and a second gRNA molecule, wherein:

(1) the first gRNA molecule is: (a) selected from the gRNA molecules of gRNA molecule embodiment 16, (b) selected from the gRNA molecules of gRNA molecule embodiment 17, (c) selected from the gRNA molecules of gRNA molecule embodiment 18, or (d) selected from the gRNA molecules of any of gRNA molecule embodiments 57-68; and (2) the second gRNA molecule includes a targeting domain that is complementary to a target sequence of the beta globin gene; or (1) the first gRNA molecule is: (a) selected from the gRNA molecules of gRNA molecule embodiment 4, (b) selected from the gRNA molecules of gRNA molecule embodiment 5, (c) selected from the gRNA molecules of gRNA molecule embodiment 6, (d) selected from the gRNA molecules of gRNA molecule embodiment 7, (e) selected from the gRNA molecules of any of gRNA molecule embodiments 41-56, (f) selected from the gRNA molecules of gRNA molecule embodiment 10, (g) selected from the gRNA molecules of gRNA molecule embodiment 11, (h) selected from the gRNA molecules of gRNA molecule embodiment 13, or (i) selected from the gRNA molecules of gRNA molecule embodiment 14; and (2) the second gRNA molecule includes a targeting domain that is complementary to a target sequence of the beta globin gene.

In embodiments, including in any of the aforementioned composition aspects and embodiments, the invention provides a composition, wherein the first gRNA molecule and the second gRNA molecule are independently selected from the gRNA molecules of any of gRNA molecule embodiments 41-68.

In embodiments of the composition, with respect to the gRNA molecule components of the composition, the composition consists of a first gRNA molecule and a second gRNA molecule.

In embodiments of the composition, each of said gRNA molecules is in a ribonuclear protein complex (RNP) with a Cas9 molecule described herein.

In embodiments, including in any of the aforementioned composition aspects and embodiments, the invention provides a composition, further including a template nucleic acid, wherein the template nucleic acid includes a nucleotide that corresponds to a nucleotide at or near the target sequence of the first gRNA molecule. In embodiments, the template nucleic acid includes nucleic acid encoding: (a) human beta globin, e.g., human beta globin including one or more of the mutations G 16D, E22A and T87Q, or fragment thereof; or (b) human gamma globin, or fragment thereof.

In embodiments, including in any of the aforementioned composition aspects and embodiments, the composition is formulated in a medium suitable for electroporation, for example, suitable for electroporation into HSPC cells. In embodiments of the composition which include one or more gRNA molecules, each of said gRNA molecules is in a RNP with a Cas9 molecule described herein, and wherein each of said RNP is at a concentration of less than about 10 uM, e.g., less than about 3 uM, e.g., less than about 1 uM, e.g., less than about 0.5 uM, e.g., less than about 0.3 uM, e.g., less than about 0.1 uM.

In another aspect, the invention provides a nucleic acid sequence that encodes one or more gRNA molecules described herein, for example, a gRNA molecule of any of the previous aspects and embodiments. In embodiments, the nucleic acid includes a promoter operably linked to the sequence that encodes the one or more gRNA molecules, for example, a promoter recognized by an RNA polymerase II or RNA polymerase III, for example, a U6 promoter or an HI promoter. In embodiments, the nucleic acid further encodes a Cas9 molecule, for example, described herein, for example, a Cas9 molecule that includes (e.g., consists of) any of SEQ ID NO: 6611, SEQ ID NO: 7821, SEQ ID NO: 7822, SEQ ID NO: 7823, SEQ ID NO: 7824, SEQ ID NO: 7825, SEQ ID NO: 7826, SEQ ID NO: 7827, SEQ ID NO: 7828, SEQ ID NO: 7829, SEQ ID NO: 7830, or SEQ ID NO: 7831. In embodiments, the nucleic acid includes a promoter operably linked to the sequence that encodes a Cas9 molecule, for example, an EF-1 promoter, a CMV IE gene promoter, an EF-1α promoter, an ubiquitin C promoter, or a phosphoglycerate kinase (PGK) promoter.

In another aspect, the invention provides a vector including the nucleic acid of any of the previous nucleic acid aspects and embodiments. In embodiments, the vector is selected from the group consisting of a lentiviral vector, an adenoviral vector, an adeno-associated viral (AAV) vector, a herpes simplex virus (HSV) vector, a plasmid, a minicircle, a nanoplasmid, and an RNA vector.

In another aspect, the invention provides a method of altering a cell (e.g., a population of cells), (e.g., altering the structure (e.g., sequence) of nucleic acid) at or near a target sequence within said cell, including contacting (e.g., introducing into) said cell (e.g., population of cells) with: 1) one or more gRNA molecules of any of the previous gRNA molecule aspects and embodiments and a Cas9 molecule (e.g., described herein); 2) one or more gRNA molecules of any of the previous gRNA molecule aspects and embodiments and nucleic acid encoding a Cas9 molecule (e.g., described herein); 3) nucleic acid encoding one or more gRNA molecules of any of the previous gRNA molecule aspects and embodiments and a Cas9 molecule (e.g., described herein); 4) nucleic acid encoding one or more gRNA molecules of any of the previous gRNA molecule aspects and embodiments and nucleic acid encoding a Cas9 molecule (e.g., described herein); 5) any of 1) to 4), above, and a template nucleic acid; 6) any of 1) to 4) above, and nucleic acid including sequence encoding a template nucleic acid; 7) the composition of any of the previous composition aspects and embodiments; or 8) the vector of any of the previous vector aspects and embodiments. In embodiments, the gRNA molecule or nucleic acid encoding the gRNA molecule, and the Cas9 molecule or nucleic acid encoding the Cas9 molecule, are formulated in a single composition. In other embodiments, the gRNA molecule or nucleic acid encoding the gRNA molecule, and the Cas9 molecule or nucleic acid encoding the Cas9 molecule, are formulated in more than one composition. In embodiments that include more than one composition, the more than one composition are delivered simultaneously or sequentially. In embodiments, the cell is an animal cell, for example, a mammalian, primate, or human cell. In embodiments, the cell, is a hematopoietic stem or progenitor cell (HSPC) (e.g., a population of HSPCs), for example, the cell is a CD34+ cell, for example, the cell is a CD34+CD90+ cell. In embodiments, the cell is disposed in a composition including a population of cells that has been enriched for CD34+ cells. In embodiments, the cell (e.g. population of cells) has been isolated from bone marrow, mobilized peripheral blood, or umbilical cord blood. In embodiments, the cell is autologous with respect to a patient to be administered said cell. In other embodiments, the cell is allogeneic with respect to a patient to be administered said cell. In embodiments, the method results in an indel at or near a genomic DNA sequence complementary to the targeting domain of the one or more gRNA molecules, for example, an indel shown on FIG. 25, Table 15, Table 26, Table 27 or Table 37, for example an indel associated with the targeting domain of the gRNA molecule as shown in FIG. 25, Table 15, Table 26, Table 27 or Table 37. In embodiments, the indel is an insertion or deletion of less than about 40 nucleotides, e.g., less than 30 nucleotides, e.g., less than 20 nucleotides, e.g., less than 10 nucleotides, for example, is a single nucleotide deletion. In embodiments, the method results in a population of cells wherein at least about 50%, e.g., at least about 60%, e.g., at least about 70%, e.g., at least about 80%, e.g., at least about 90% (e.g., at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99%) of the cells of the population have been altered, e.g., include an indel. In embodiments, the method (e.g., the method performed on a population of cells, e.g., described herein) results in a cell (e.g., population of cells) that is capable of differentiating into a differentiated cell of an erythroid lineage (e.g., a red blood cell), and wherein said differentiated cell exhibits an increased level of fetal hemoglobin, e.g., relative to an unaltered cell (e.g., population of cells). In embodiments, the method results in a population of cells that is capable of differentiating into a population of differentiated cells, e.g., a population of cells of an erythroid lineage (e.g., a population of red blood cells), and wherein said population of differentiated cells has an increased fraction of F cells (e.g., at least about 15%, at least about 20%, at least about 25%, at least about 30%, or at least about 40% higher) e.g., relative to a population of unaltered cells. In embodiments, the method results in a cell that is capable of differentiating into a differentiated cell, e.g., a cell of an erythroid lineage (e.g., a red blood cell), and wherein said differentiated cell produces at least about 6 picograms (e.g., at least about 7 picograms, at least about 8 picograms, at least about 9 picograms, at least about 10 picograms, or from about 8 to about 9 picograms, or from about 9 to about 10 picograms) fetal hemoglobin per cell. In embodiments, the method is performed ex vivo. In other embodiments, the method is performed in vivo.

In another aspect, the invention provides a cell, altered by the method of altering a cell of any of the previous method aspects and embodiments.

In another aspect, the invention provides a cell, obtainable the method of altering a cell of any of the previous method aspects and embodiments.

In another aspect, the invention provides a cell, including a first gRNA molecule, e.g., described herein, e.g., of any of the previous gRNA molecule aspects and embodiments, or a composition, e.g., described herein, e.g., of any of the previous composition aspects and embodiments, a nucleic acid, e.g., described herein, e.g., of any of the previous nucleic acid aspects and embodiments, or a vector, e.g., described herein, e.g., of any of the previous vector aspects and embodiments. In embodiments, the cell further includes a Cas9 molecule, e.g., described herein, for example, a Cas9 molecule that includes, e.g., consists of, any of SEQ ID NO: 6611, SEQ ID NO: 7821, SEQ ID NO: 7822, SEQ ID NO: 7823, SEQ ID NO: 7824, SEQ ID NO: 7825, SEQ ID NO: 7826, SEQ ID NO: 7827, SEQ ID NO: 7828, SEQ ID NO: 7829, SEQ ID NO: 7830, or SEQ ID NO: 7831. In embodiments, the cell includes, has included, or will include a second gRNA molecule, e.g., described herein, e.g., of any of the previous gRNA molecule aspects and embodiments, or a nucleic acid encoding a second gRNA molecule, e.g., described herein, e.g., of any of the previous gRNA molecule aspects and embodiments, wherein the first gRNA molecule and second gRNA molecule include nonidentical targeting domains. In embodiments, expression of fetal hemoglobin is increased in said cell or its progeny (e.g., its erythroid progeny, e.g., its red blood cell progeny) relative to a cell or its progeny of the same cell type that has not been modified to include a gRNA molecule. In embodiments, the cell is capable of differentiating into a differentiated cell, e.g., a cell of an erythroid lineage (e.g., a red blood cell), and wherein said differentiated cell exhibits an increased level of fetal hemoglobin, e.g., relative to a cell of the same type that has not been modified to include a gRNA molecule. In embodiments, the differentiated cell (e.g., cell of an erythroid lineage, e.g., red blood cell) produces at least about 6 picograms (e.g., at least about 7 picograms, at least about 8 picograms, at least about 9 picograms, at least about 10 picograms, or from about 8 to about 9 picograms, or from about 9 to about 10 picograms) fetal hemoglobin, e.g., relative to a cell of the same type that has not been modified to include a gRNA molecule. In embodiments, the cell has been contacted, e.g., contacted ex vivo, with a stem cell expander, e.g., described herein, e.g., a stem cell expander that is compound 1, compound 2, compound 3, compound 4, or a combination thereof (e.g., compound 1 and compound 4), for example, a stem cell expander that is compound 4. In embodiments, including in any of the aforementioned aspects and embodiments, the cell includes an indel at or near a genomic DNA sequence complementary to the targeting domain of the gRNA molecule (as described herein, e.g., a gRNA molecule of any of the aforementioned aspects and embodiments) introduced therein, for example, an indel shown on FIG. 25, Table 15, Table 26, Table 27 or Table 37, for example an indel shown on FIG. 25, Table 15, Table 26, Table 27 or Table 37 that is associated with the gRNA molecule (as described herein, e.g., a gRNA molecule of any of the aforementioned aspects and embodiments) introduced therein. In embodiments, the indel is an insertion or deletion of less than about 40 nucleotides, e.g., less than 30 nucleotides, e.g., less than 20 nucleotides, e.g., less than 10 nucleotides, for example, the indel is a single nucleotide deletion. In embodiments, including in any of the aforementioned cell aspects and embodiments, the cell is an animal cell, for example, the cell is a mammalian, a primate, or a human cell. In embodiments, including in any of the aforementioned cell aspects and embodiments, the cell is a hematopoietic stem or progenitor cell (HSPC) (e.g., a population of HSPCs), for example, the cell is a CD34+ cell, for example, the cell is a CD34+CD90+ cell. In embodiments, including in any of the aforementioned cell aspects and embodiments, the cell (e.g. population of cells) has been isolated from bone marrow, mobilized peripheral blood, or umbilical cord blood. In embodiments, including in any of the aforementioned cell aspects and embodiments, the cell is autologous with respect to a patient to be administered said cell. In embodiments, the cell is allogeneic with respect to a patient to be administered said cell.

In another aspect, the invention provides a population of cells including the cell of any of the previous cell aspects and embodiments. In embodiments, at least about 50%, e.g., at least about 60%, e.g., at least about 70%, e.g., at least about 80%, e.g., at least about 90% (e.g., at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99%) of the cells of the population are a cell according to any of the previous cell aspects and embodiments. In embodiments, the population of cells is capable of differentiating into a population of differentiated cells, e.g., a population of cells of an erythroid lineage (e.g., a population of red blood cells), and wherein said population of differentiated cells has an increased fraction of F cells (e.g., at least about 15%, at least about 20%, at least about 25%, at least about 30%, or at least about 40% higher) e.g., relative to a population of unmodified cells of the same type. In embodiments, the F cells of the population of differentiated cells produce an average of at least about 6 picograms (e.g., at least about 7 picograms, at least about 8 picograms, at least about 9 picograms, at least about 10 picograms, or from about 8 to about 9 picograms, or from about 9 to about 10 picograms) fetal hemoglobin per cell. In embodiments, the population includes: 1) at least 1e6 CD34+ cells/kg body weight of the patient to whom the cells are to be administered; 2) at least 2e6 CD34+ cells/kg body weight of the patient to whom the cells are to be administered; 3) at least 3e6 CD34+ cells/kg body weight of the patient to whom the cells are to be administered; 4) at least 4e6 CD34+ cells/kg body weight of the patient to whom the cells are to be administered; or 5) from 2e6 to 10e6 CD34+ cells/kg body weight of the patient to whom the cells are to be administered. In embodiments, at least about 40%, e.g., at least about 50%, (e.g., at least about 60%, at least about 70%, at least about 80%, or at least about 90%) of the cells of the population are CD34+ cells. In embodiments, at least about 10%, e.g., at least about 15%, e.g., at least about 20%, e.g., at least about 30% of the cells of the population are CD34+CD90+ cells. In embodiments, the population of cells is derived from bone marrow, peripheral blood (e.g., mobilized peripheral blood), umbilical cord blood, or induced pluripotent stem cells (iPSCs). In a preferred embodiment, the population of cells is derived from bone marrow. In embodiments, the population of cells includes, e.g., consists of, mammalian cells, e.g., human cells. In embodiments, the population of cells is autologous relative to a patient to which it is to be administered. In other embodiments, the population of cells is allogeneic relative to a patient to which it is to be administered.

In another aspect, the invention provides a composition including a cell of any of the previous cell aspects and embodiments, or the population of cells of any of previous population of cell aspects and embodiments. In embodiments, the composition includes a pharmaceutically acceptable medium, e.g., a pharmaceutically acceptable medium suitable for cryopreservation.

In another aspect, the invention provides a method of treating a hemoglobinopathy, including administering to a patient a cell of any of the previous cell aspects and embodiments, a population of cells of any of previous population of cell aspects and embodiments, or a composition of any of the previous composition aspects and embodiments. In embodiments, the hemoglobinopathy is a thalassemia, for example, beta-thalassemia, or sickle cell disease.

In another aspect, the invention provides a method of increasing fetal hemoglobin expression in a mammal, including administering to a patient a cell of any of the previous cell aspects and embodiments, a population of cells of any of previous population of cell aspects and embodiments, or a composition of any of the previous composition aspects and embodiments.

In another aspect, the invention provides a method of preparing a cell (e.g., a population of cells) including: (a) providing a cell (e.g., a population of cells) (e.g., a HSPC (e.g., a population of HSPCs)); (b) culturing said cell (e.g., said population of cells) ex vivo in a cell culture medium including a stem cell expander; and (c) introducing into said cell a first gRNA molecule (e.g., described herein, for example, a gRNA molecule of any of the previous gRNA molecule aspects and embodiments), a nucleic acid molecule encoding a first gRNA molecule (e.g., described herein, for example, a gRNA molecule of any of the previous gRNA molecule aspects and embodiments), a composition (e.g., described herein, for example, a composition of any of the previous composition aspects and embodiments), a nucleic acid (e.g., described herein, for example, a nucleic acid of any of the previous nucleic acid aspects and embodiments), or a vector (e.g., described herein, for example, a vector of any of the previous vector aspects and embodiments). In embodiments of said method, after said introducing of step (c), said cell (e.g., population of cells) is capable of differentiating into a differentiated cell (e.g., population of differentiated cells), e.g., a cell of an erythroid lineage (e.g., population of cells of an erythroid lineage), e.g., a red blood cell (e.g., a population of red blood cells), and wherein said differentiated cell (e.g., population of differentiated cells) produces increased fetal hemoglobin, e.g., relative to the same cells which have not been subjected to step (c). In embodiments, including in any of the aforementioned method aspects and embodiments, the stem cell expander is compound 1, compound 2, compound 3, compound 4 or a combination thereof (e.g., compound 1 and compound 4), for example, is compound 4. In embodiments, including in any of the aforementioned method aspects and embodiments, the cell culture medium includes thrombopoietin (Tpo), Flt3 ligand (Flt-3L), and human stem cell factor (SCF). In embodiments, including in any of the aforementioned method aspects and embodiments, the cell culture medium further includes human interleukin-6 (IL-6). In embodiments, including in any of the aforementioned method aspects and embodiments, the cell culture medium includes thrombopoietin (Tpo), Flt3 ligand (Flt-3L), and human stem cell factor (SCF) each at a concentration ranging from about 10 ng/mL to about 1000 ng/mL, for example, each at a concentration of about 50 ng/mL, e.g., at a concentration of 50 ng/mL. In embodiments, including in any of the aforementioned method aspects and embodiments, the cell culture medium includes human interleukin-6 (IL-6) at a concentration ranging from about 10 ng/mL to about 1000 ng/mL, for example, at a concentration of about 50 ng/mL, e.g., at a concentration of 50 ng/mL. In embodiments, including in any of the aforementioned method aspects and embodiments, the cell culture medium includes a stem cell expander at a concentration ranging from about 1 nM to about 1 mM, for example, at a concentration ranging from about 1 uM to about 100 uM, for example, at a concentration ranging from about 50 uM to about 75 uM, for example, at a concentration of about 50 uM, e.g., at a concentration of 50 uM, or at a concentration of about 75 uM, e.g., at a concentration of 75 uM. In embodiments, including in any of the aforementioned method aspects and embodiments, the culturing of step (b) includes a period of culturing before the introducing of step (c), for example, the period of culturing before the introducing of step (c) is at least 12 hours, e.g., is for a period of about 1 day to about 3 days, e.g., is for a period of about 1 day to about 2 days, e.g., is for a period of about 2 days. In embodiments, including in any of the aforementioned method aspects and embodiments, the culturing of step (b) includes a period of culturing after the introducing of step (c), for example, the period of culturing after the introducing of step (c) is at least 12 hours, e.g., is for a period of about 1 day to about 10 days, e.g., is for a period of about 1 day to about 5 days, e.g., is for a period of about 2 days to about 4 days, e.g., is for a period of about 2 days or is for a period of about 3 days or is for a period of about 4 days. In embodiments, including in any of the aforementioned method aspects and embodiments, the population of cells is expanded at least 4-fold, e.g., at least 5-fold, e.g., at least 10-fold, e.g., relative to cells which are not cultured according to step (b). In embodiments, including in any of the aforementioned method aspects and embodiments, the introducing of step (c) includes an electroporation, for example, an electroporation that includes 1 to 5 pulses, e.g., 1 pulse, and wherein each pulse is at a pulse voltage ranging from 700 volts to 2000 volts and has a pulse duration ranging from 10 ms to 100 ms. In embodiments, including in any of the aforementioned method aspects and embodiments, the electroporation includes, for example, consists of, 1 pulse. In embodiments, including in any of the aforementioned method aspects and embodiments, the pulse voltage ranges from 1500 to 1900 volts, e.g., is 1700 volts. In embodiments, including in any of the aforementioned method aspects and embodiments, the pulse duration ranges from 10 ms to 40 ms, e.g., is 20 ms. In embodiments, including in any of the aforementioned method aspects and embodiments, the cell (e.g., population of cells) provided in step (a) is a human cell (e.g., a population of human cells). In embodiments, including in any of the aforementioned method aspects and embodiments, the cell (e.g., population of cells) provided in step (a) is isolated from bone marrow, peripheral blood (e.g., mobilized peripheral blood), umbilical cord blood, or induced pluripotent stem cells (iPSCs), preferably bone marrow. In embodiments, including in any of the aforementioned method aspects and embodiments, the cell (e.g., population of cells) provided in step (a) is isolated from bone marrow, e.g., is isolated from bone marrow of a patient suffering from a hemoglobinopathy. In embodiments, including in any of the aforementioned method aspects and embodiments, the population of cells provided in step (a) is enriched for HSPCs, e.g., CD34+ cells. In embodiments, including in any of the aforementioned method aspects and embodiments, subsequent to the introducing of step (c), the cell (e.g., population of cells) is cryopreserved. In embodiments, including in any of the aforementioned method aspects and embodiments, subsequent to the introducing of step (c), the cell (e.g., population of cells) includes an indel at or near a genomic DNA sequence complementary to the targeting domain of the first gRNA molecule, for example, an indel shown on FIG. 25, Table 15, Table 26, Table 27 or Table 37, for example an indel shown in FIG. 25, Table 15, Table 26, Table 27 or Table 37 as associated with the first gRNA molecule. In embodiments, including in any of the aforementioned method aspects and embodiments, after the introducing of step (c), at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98% or at least about 99% of the cells of the population of cells include an indel at or near a genomic DNA sequence complementary to the targeting domain of the first gRNA molecule, for example, an indel shown on FIG. 25, Table 15, Table 26, Table 27 or Table 37, for example an indel shown in FIG. 25, Table 15, Table 26, Table 27 or Table 37 as associated with the first gRNA molecule.

In another aspect, the invention provides a cell (e.g., population of cells), obtainable by the method of preparing a cell of any of the previous aspects and embodiments. In another aspect, the invention provides a method of treating a hemoglobinopathy (for example a thalassemia (e.g., beta-thalassemia) or sickle cell disease), including administering to a human patient a composition including said cell (e.g., population of cells). In another aspect, the invention provides a method of increasing fetal hemoglobin expression in a human patient, including administering to said human patient a composition including said cell (e.g., population of cells). In embodiments, the human patient is administered a composition including at least about 1e6 cells (e.g., CD34+ cells, e.g., cells obtainable by a method of preparing a cell of any of the previous aspects and embodiments) per kg body weight of the human patient, e.g., at least about 1e6 CD34+ cells obtainable by a method of preparing a cell of any of the previous aspects and embodiments per kg body weight of the human patient. In embodiments, the human patient is administered a composition including at least about 2e6 cells (e.g., CD34+ cells, e.g., cells obtainable by a method of preparing a cell of any of the previous aspects and embodiments) per kg body weight of the human patient, e.g., at least about 2e6 CD34+ cells obtainable by a method of preparing a cell of any of the previous aspects and embodiments per kg body weight of the human patient. In embodiments, the human patient is administered a composition including from about 2e6 to about 10e6cells (e.g., CD34+ cells, e.g., cells obtainable by a method of preparing a cell of any of the previous aspects and embodiments) per kg body weight of the human patient, e.g., at least about 2e6 to about 10e6 CD34+ cells obtainable by a method of preparing a cell of any of the previous aspects and embodiments per kg body weight of the human patient.

In another aspect, the invention provides a gRNA molecule described herein, for example, a gRNA molecule of any of the previous gRNA molecule aspects and embodiments, a composition described herein, for example, a composition of any of the previous composition aspects and embodiments, a nucleic acid described herein, for example, a nucleic acid of any of the previous nucleic acid aspects and embodiments, a vector described herein, for example, a vector of any of the previous vector aspects and embodiments, a cell described herein, for example, a cell of any of the previous cell aspects and embodiments, or a population of cells described herein, for example, a population of cells of any of the previous population of cell aspects and embodiments, for use as a medicament.

In another aspect, the invention provides a gRNA molecule described herein, for example, a gRNA molecule of any of the previous gRNA molecule aspects and embodiments, a composition described herein, for example, a composition of any of the previous composition aspects and embodiments, a nucleic acid described herein, for example, a nucleic acid of any of the previous nucleic acid aspects and embodiments, a vector described herein, for example, a vector of any of the previous vector aspects and embodiments, a cell described herein, for example, a cell of any of the previous cell aspects and embodiments, or a population of cells described herein, for example, a population of cells of any of the previous population of cell aspects and embodiments, for use in the manufacture of a medicament.

In another aspect, the invention provides a gRNA molecule described herein, for example, a gRNA molecule of any of the previous gRNA molecule aspects and embodiments, a composition described herein, for example, a composition of any of the previous composition aspects and embodiments, a nucleic acid described herein, for example, a nucleic acid of any of the previous nucleic acid aspects and embodiments, a vector described herein, for example, a vector of any of the previous vector aspects and embodiments, a cell described herein, for example, a cell of any of the previous cell aspects and embodiments, or a population of cells described herein, for example, a population of cells of any of the previous population of cell aspects and embodiments, for use in the treatment of a disease.

In another aspect, the invention provides a gRNA molecule described herein, for example, a gRNA molecule of any of the previous gRNA molecule aspects and embodiments, a composition described herein, for example, a composition of any of the previous composition aspects and embodiments, a nucleic acid described herein, for example, a nucleic acid of any of the previous nucleic acid aspects and embodiments, a vector described herein, for example, a vector of any of the previous vector aspects and embodiments, a cell described herein, for example, a cell of any of the previous cell aspects and embodiments, or a population of cells described herein, for example, a population of cells of any of the previous population of cell aspects and embodiments, for use in the treatment of a disease, wherein the disease is a hemoglobinopathy, for example a thalassemia (e.g., beta-thalassemia) or sickle cell disease.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1: Cas9 editing of the Bcl11a +58 erythroid enhancer region. Fraction of editing detected by NGS in HEK-293 Cas9GFP 24 h post-delivery of crRNA targeting the +58 enhancer region and trRNA by lipofection. Each dot indicates a different crRNA, the trRNA was held constant. Genomic coordinates indicate location on Chromosome 2, e.g., in reference to hg38. (n=1)

FIG. 2: Cas9 editing of the Bcl11a +62 erythroid enhancer region. Fraction of editing detected by NGS in HEK-293 Cas9GFP 24 h post-delivery of crRNA targeting the +62 enhancer region and trRNA by lipofection. Each dot indicates a different crRNA, the trRNA was held constant. Genomic coordinates indicate location on Chromosome 2, e.g., in reference to hg38. (n=1)

FIG. 3. Gating strategy for selection of cells after introduction of the Cas9 editing system.

FIG. 4. Agarose gel electrophoresis of gene fragments from Cas9 editing system-treated CD34+ cells (shown are both CD34+CD90+ and CD34+CD90− cell populations, together with reference unsorted cells). The upper band represents uncleaved homoduplex DNA and the lower bands indicate cleavage products resulting from heteroduplex DNA. The far left lane is a DNA ladder. Band intensity was calculated by peak integration of unprocessed images by ImageJ software. % gene modification (indel) was calculated as follows: % gene modification=100×(1−(1−fraction cleaved)^(1/2)), and is indicated below each corresponding lane of the gel.

FIG. 5. Erythroid enhancer region showing the sites of genomic DNA targeted by sgRNA molecules comprising targeting domains complimentary to the underlined nucleotides.

FIG. 6A/6B. NGS results for indel formation by sgEH1 (CR00276) (A) or sgEH2 (CR00275) (B) in CD34+ HSC cells. Insertions are in uppercase. Deletions are indicated by a dashed line. Regions of microhomology near the cutting site are highlighted in bold underline.

FIG. 6C/6D. NGS results for indel formation by sgEH8 (CR00273) (C) or sgEH9 (CR00277) (D) in CD34+ HSC cells. Insertions are in uppercase. Deletions are indicated by a dashed line. Regions of microhomology near the cutting site are highlighted in bold underline.

FIG. 7. NGS results and indel pattern formation across multiple donors for g7, g8 and g2. The sequences of the top 3 indels from two biological replicate experiments using g7 and g8 were identical, and the sequence of the top 3 indels using g2 were identical to those from a previous experiment.

FIG. 8. NGS results and indel pattern formation using a modified gRNA scaffold (BC). The sequences of the top 3 indels from these experiments are identical to those formed when using the standard gRNA scaffold.

FIG. 9. Comparison of indel pattern across different delivery methods. AVG % refers to the % of NGS reads exhibiting the indel indicated (Average of 2 experiments).

FIG. 10. Indel formation by co-introduction of g7 gRNA and g8 gRNA with either a non-extended flagpole region (“reg”) or with a first flagpole extension and first tracr extension (“BC”). PAM sequences for the two gRNAs are boxed.

FIG. 11: Top gRNA sequences directed to +58 enhancer region of BCL11a gene in CD34+ cells, as measured by NGS (n=3).

FIG. 12: Top gRNA sequences directed to +62 enhancer region of BCL11a gene in CD34+ cells, as measured by NGS (n=3).

FIG. 13: Predicted excision sizes when 2 gRNA molecules targeting the BCL11a +62 enhancer locus are introduced into HEK293_Cas9 cells, when either CR00187 (light grey bars) or CR00202 (dark grey bars) is held constant and co-inserted into the cells with a second gRNA molecule including the targeting domain of the gRNA indicated.

FIG. 14: Excision of genomic DNA within the +62 enhancer of BCL11a by addition of gRNA molecules including the targeting domain of CR00187 and the second gRNA molecule indicated in the graph. Stars (*) indicate excision observed at a frequency greater than 30%; Carats (̂) indicate excision observed at a lower frequency (<30%). Those predicted excision products resulting in a fragment less than 50 nt could not be distinguished.

FIG. 15: Excision of genomic DNA within the +62 enhancer of BCL11a by addition of gRNA molecules including the targeting domain of CR00202 and the second gRNA molecule indicated in the graph. Stars (*) indicate excision observed at a frequency greater than 30%; Carats (̂) indicate excision observed at lower frequency (<30%).

FIG. 16: % indel formation by 192 gRNA molecules targeted to the French HPFH region (Sankaran V G et al. A functional element necessary for fetal hemoglobin silencing. NEJM (2011) 365:807-814.)

FIG. 17. Experimental scheme of Cas9:gRNA ribonucleoprotein (Cas9-RNP) delivery to primary human CD34+ HSPC for genome editing, followed by genetic and phenotypic characterization.

FIG. 18. Cell viability following mock electroporation or electroporation of Cas9-RNP complexes into CD34+ HSPC. The HSPC were expanded in vitro for 48 hours after electroporation of RNP complexes and the cell viability monitored and percent viability determined. The names of gRNAs used to make RNP complexes are shown on x-axis and the corresponding cell viabilities on y-axis. The CRxxxx identifier indicates the targeting domain of the gRNA molecule.

FIG. 19. Mismatch detection using T7 endonuclease assay Human HSC were electroporated to deliver RNP complexes to introduce indels into +58 DHS region of BCL11A erythroid enhancer by NHEJ. PCR amplicons spanning the target region was subjected to the T7E1 assay and the resulting fragments analyzed by 2% agarose gel electrophoresis. Regions of +58 erythroid enhancer BCL11A were disrupted by both guide RNA formats (dual guide RNA—black; single guide RNA—gray (bottom graph and g7BCL11a-BC(1) and g7BCL11A-BC(2) from top graph)). The intensities of DNA bands were estimated by the ImageJ software (http://rsb.info.nih.gov/ij/) to determine the percent of edited alleles. Names of gRNAs used and corresponding gene editing efficiencies determined from mismatch detection assay are also shown in the table below the gel image.

FIG. 20: Percent allele editing by next generation sequencing. Labels are as described for FIGS. 18 and 19.

FIG. 21. Colony forming cell (CFC) unit assay showing colony number and types of colonies observed for five select gRNAs. The HSPCs genome edited at the +58 erythroid enhancer were plated in methylcellulose and clonal colonies classified and counted based on the number and types of mature cells using morphological and phenotypic criteria using STEMvision. The colonies were classified into colony forming unit-erythroid (CFU-E), burst forming unit-erythroid (BFU-E), colony-forming unit-granulocyte/macrophage (CFU-GM) and colony-forming unit-granulocyte/erythrocyte/macrophage/megakaryocyte (CFU-GEMM).

FIG. 22. Kinetics of cell division during erythroid differentiation. Total number of cells determined on day 0, 7, 14 and 21 during erythroid differentiation and the fold cell expansion calculated.

FIG. 23. BCL11A, gamma and beta-globin mRNA levels in genome edited and erythroid differentiated HSC. Relative mRNA expression of BCL11A, gamma- and beta-globin chains in unilineage erythroid cultures were quantified by real time PCR. Transcript levels were normalized against human GAPDH transcript levels.

FIG. 24A. Efficient editing of HSC obtained with dual gRNA/cas9 system for disruption of BCL11a enhancer (+58) resulted in high levels of induction of HbF. The HSC 48 hours after electroporation were subjected to in vitro erythroid differentiation and HbF expression was measured. The percent of HbF positive cells (F-cells) was monitored by FACS analysis at days 7, 14 and 21. Data shown in this figure was generated with dgRNA systems where the dgRNA included the indicated targeting domain.

FIG. 24B. Efficient editing of HSC obtained with sgRNA/cas9 system for disruption of BCL11a enhancer (+58) resulted in high levels of induction of HbF. The HSC 48 hours after electroporation were subjected to in vitro erythroid differentiation and HbF expression was measured. The percent of HbF positive cells (F-cells) was monitored by FACS analysis at days 7, 14 and 21. Data shown in this figure was generated with sgRNA systems where the sgRNA included the indicated targeting domain.

FIG. 25: Indel pattern produced in HSPCs by gRNAs including the indicated targeting domain.

FIG. 26A: Phenotyping of edited and unedited cultures in CD34+ cell expansion medium by cell surface marker staining. All gRNA molecules were tested in the dgRNA format. The Tmcr used was SEQ ID NO: 7808, and the crRNA had the following format and sequence with 2′O-Methyl (m) and Phosphorothioate Bond (*) modifications indicated: mN*mN*mN*rNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrGrUrUrUrUrArGrArGrCrUrArU*mG*m C*mU, where N's are the residues of the indicated targeting domain. Shown are representative dot plots showing the fluorescence of cells stained with each antibody panel or corresponding isotype controls as described in Materials and Methods. Cells shown were pre-gated on the viable cell population by forward and side scatter properties and DAPI (4′,6-Diamidino-2-Phenylindole) discrimination. The percentage of each cell population named at the top of the plot was determined by the gate indicated by the bold lined box.

FIG. 26B: Phenotyping of edited and unedited cultures in CD34+ cell expansion medium by cell surface marker staining. All gRNA molecules were tested in the dgRNA format. The Tmcr used was SEQ ID NO: 7808, and the crRNA had the following format and sequence with 2′O-Methyl (m) and Phosphorothioate Bond (*) modifications indicated: mN*mN*mN*rNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrGrUrUrUrUrArGrArGrCrUrArU*mG*m C*mU, where N's are the residues of the indicated targeting domain Shown is the percentage of each named cell population in edited and unedited cultures. Targeting domain of the edited cultures is as indicated.

FIG. 27. % F cells in erythrocytes differentiated from populations of CD34+ cells edited with RNPs comprising dgRNAs targeting two sites within the HPFH region. “g2” is the positive control (targeting domain to a coding region of BCL11a gene); “cntrl” is negative control (introduction of Cas9 only).

FIG. 28A. % Editing as determined by NGS in CD34+ HSPCs at day 2 following electroporation of RNP comprising the indicated dgRNA (unmod or modified as indicated). Controls include dgRNA comprising the targeting domain of CR00317 unmodified (CR00317-m), or electroporation in buffer only (No Cas9 or gRNA; “Mock”).

FIG. 28B. % Editing as determined by NGS in CD34+ HSPCs at day 2 following electroporation of RNP comprising the indicated dgRNA (unmod or modified as indicated). Controls include electroporation in buffer only (No Cas9 or gRNA; “Mock”).

FIG. 29. % Editing as determined by NGS in CD34+ HSPCs at day 2 following electroporation of RNP comprising the indicated sgRNA (unmod or modified as indicated. In each case the number corresponds to the CRxxxxxx identifier of the targeting domain, for example, Unmod sg312 refers to unmodified sgRNA comprising the targeting domain of CR00312). Controls include electroporation of Cas9 protein only (“Cas9”), electroporation with buffer only (“mock”), or with no electroporation (“WT”).

FIG. 30A. Normalized % Erythrocytes (% F cells in “Mock” subtracted) that are HbF+ after electroporation of CD34+ HSPCs with RNP comprising the indicated dgRNA (unmod or modified as indicated) and then induced to differentiate by culture in erythroid differentiation medium. Controls include electroporation of buffer only (“mock”).

FIG. 30B. Normalized % Erythrocytes (% F cells in “Mock” subtracted) that are HbF+ after electroporation of CD34+ HSPCs with RNP comprising the indicated dgRNA (unmod or modified as indicated) and then in induced to differentiate by culture in erythroid differentiation medium. Controls include electroporation of buffer only (“mock”).

FIG. 31. Normalized % Erythrocytes (% F cells in “Mock” subtracted) that are HbF+ after electroporation of CD34+ HSPCs with RNP comprising the indicated sgRNA (unmod or modified as indicated. In each case the number corresponds to the CRxxxxxx identifier of the targeting domain, for example, Unmod sg312 refers to unmodified sgRNA comprising the targeting domain of CR00312) and then in induced to differentiate by culture in erythroid differentiation medium. Controls include electroporation of Cas9 protein and tracr only (“Cas9+TracRNA only”), electroporation with buffer only (“Cells only+Pulse”), or with no electroporation (“Cells only no pulse”).

FIG. 32. Fold total cell expansion in culture at day 14 after erythroid differentiation after electroporation of RNP comprising the indicated sgRNA (in each case, the number corresponds to the CRxxxxxx identifier of the targeting domain, for example, Unmod sg312 refers to unmodified sgRNA comprising the targeting domain of CR00312) into CD34+ cells. Controls include electroporation of Cas9 protein and tracr only (“Cas9+TracRNA only”), electroporation with buffer only (“Cells only+Pulse”), or with no electroporation (“Cells only no pulse”).

FIG. 33. Assessment of potential off-target sites cleaved by Cas9 directed by dgRNA molecules targeting the BCL11a enhancer region. Triangles represent the on-target site while open circles represent a potential off-target site for each guide RNA tested.

FIG. 34. Editing efficiency at targeted B2M locus in CD34+ hematopoietic stem cells by different Cas9 variants, as evaluated by NGS and Flow cytometry. NLS=SV40 NLS; His6 or His8 refers to 6 or 8 histidine residues, respectively; TEV=tobacco etch virus cleavage site; Cas9=wild type S. pyogenes Cas9—mutations or variants are as indicated).

FIG. 35. Data show fold increase in cell number after a total of 10 days of culturing in expansion medium (3 days of culturing prior to electroporation and 7 days of culturing following electroporation). With all the guide RNAs tested, including both single and dual guide RNA formats, cell expansion ranged from 2-7 fold. CR00312 and CR001128, indicated by arrows, demonstrated a 3-6 fold increase after 10 days of cell expansion. Lables “Crxxxx” refer to dgRNA having the indicated targeting domain; “sgxxxx” refer to sgRNA having the targeting domain of the CRxxxxx identifier with the same number (e.g., sg312 has the targeting domain of CR00312); “Unmod” indicates no modification to theRNA(s); “O'MePS”, when used in relation to a dgRNA refers to a crRNA which has three 3′ and three 5′ 2′-OMe modifications and phosphorothioate bonds, paired with an unmodified tracr; “O'MePS”, when used in relation to a sgRNA refers to gRNA which has three 5′-terminal 2′-OMe modifications and phosphorothioate bonds, three 3′-terminal phosphorothioate bonds, and three 2′OMe modifications of the 4^(th)-to-last, 3^(rd)-to-last and 2^(nd)-to-last 3′ nucleotides.

FIG. 36. Gating strategy to distinguish different HSPC subpopulations.

FIG. 37. Frequency of each hematopoietic subset after 48 hours ex vivo culture in the indicated medium (STF modified with IL6, Compound 4, or both IL6 and Compound 4), but before electroporation of a CRISPR system. STF=StemSpan SFEM.

FIG. 38. Frequency of each hematopoietic subset 7 days after electroporation introducing a CRISPR system targeting the +58 enhancer of BCL11a, cultured in the indicated medium (STF modified with IL6, Compound 4, or both IL6 and Compound 4). STF=StemSpan SFEM.

FIG. 39A. Cell viability upon gene editing using different RNP concentrations, with RNP containing dgRNAs targeting the +58 region.

FIG. 39B. Cell viability upon gene editing using different RNP concentrations, with RNP containing sgRNAs targeting the +58 region.

FIG. 40A. Gene editing efficiency measured by NGS upon gene editing using different RNP concentrations, with RNP containing dgRNAs targeting the +58 region.

FIG. 40B Gene editing efficiency measured by NGS upon gene editing using different RNP concentrations, with RNP containing sgRNAs targeting the +58 region.

FIG. 41A. Percentage of HbF induction measured by flow cytometry upon gene editing using different RNP concentrations, with RNP containing dgRNAs targeting the +58 region.

FIG. 41B Percentage of HbF induction measured by flow cytometry upon gene editing using different RNP concentrations, with RNP containing sgRNAs targeting the +58 region.

FIG. 42A. Gene editing efficiencies of RNPs with different Cas9 proteins. Gene editing was performed using different Cas9 variants (listed on the X-axis) coupled with either the unmodified version of sgRNA CR00312 and sgRNA CR001128, or a modified version of sgRNA CR00312 and sgRNA CR001128. Edited cells were subjected to NGS to determine % edit (Y-axis).

FIG. 42B. Induction of HbF+ cells upon gene editing using different Cas9 proteins. Gene editing was performed using different Cas9 variants (listed on the X-axis) coupled with either the unmodified version of sgRNA CR00312 and sgRNA CR001128, or a modified version of sgRNA CR00312 and sgRNA CR001128. Edited cells were differentiated into erythroid lineage and HbF production assessed by flow cytometry using an anti-HbF antibody conjugated with fluorophore.

FIG. 43. % Editing as determined by NGS in CD34+ HSPCs by electroporation of RNP comprising the indicated dgRNA or sgRNA (unmod or modified as indicated) (labels refer to the gRNA sequences as indicated in Table 36). Editing was determined at either 2 days (black bars) or 6 days (gray bars) post-electroporation. Less than 1.5% editing was detected at each site after control electroporation of Cas9 protein and Tracr only (“none”, data not shown). Mean+standard deviation of 2 electroporation replicates is shown.

FIG. 44. Percent of viable cells that are CD71+ after electroporation into CD34+ HSPCs of RNP comprising the indicated dgRNA or sgRNA (unmod or modified as indicated) (labels refer to the gRNA sequences as indicated in Table 36) and culture in erythroid differentiation conditions for 7 days. After electroporation, cells were maintained by Protocol 1 (black bars) or Protocol 2 (gray bars), as described in Example 4.7. Controls include electroporation of Cas9 protein and Tracr only (“none”). Mean+standard deviation of 2 electroporation replicates is shown.

FIG. 45. Percent of erythroid cells that are HbF+ after electroporation into CD34+ HSPCs of RNP comprising the indicated dgRNA or sgRNA (unmod or modified as indicated) (labels refer to the gRNA sequences as indicated in Table 36) and culture in erythroid differentiation conditions for 7 days. After electroporation, cells were maintained by Protocol 1 (black bars) or Protocol 2 (gray bars), as described in Example 4.7. Controls include electroporation of Cas9 protein and Tracr only (“none”). Mean+standard deviation of 2 electroporation replicates is shown.

FIG. 46. Percent of cells that are HbF+ after electroporation into CD34+ HSPCs of RNP comprising the indicated dgRNA or sgRNA (unmod or modified as indicated) (labels refer to the gRNA sequences as indicated in Table 36) and cultured in erythroid differentiation conditions for 14 days. After electroporation, cells were maintained by Protocol 1 (black bars) or Protocol 2 (gray bars), as described in Example 4.7. Controls include electroporation of Cas9 protein and Tracr only (“none”). Mean+standard deviation of 2 electroporation replicates is shown.

FIG. 47. Percent of cells that are HbF+ after electroporation into CD34+ HSPCs of RNP comprising the indicated dgRNA or sgRNA (unmod or modified as indicated) (labels refer to the gRNA sequences as indicated in Table 36) and cultured in erythroid differentiation conditions for 21 days. After electroporation, cells were maintained by Protocol 1 (black bars) or Protocol 2 (gray bars), as described in Example 4.7. Controls include electroporation of Cas9 protein and Tracr only (“none”). Mean+standard deviation of 2 electroporation replicates is shown.

FIG. 48. Fold total cell expansion in erythroid differentiation culture for 7 (black bars) or 21 days (black bars) after electroporation into CD34+ HSPCs of RNP comprising the indicated dgRNA or sgRNA (unmod or modified as indicated) (labels refer to the gRNA sequences as indicated in Table 36). After electroporation, cells were maintained by Protocol 2, as described in Example 4.7. Controls include electroporation of Cas9 protein and Tracr only (“none”). Mean+standard deviation of 2 electroporation replicates is shown.

FIG. 49. Assessment of potential off-target sites cleaved by Cas9 directed by dgRNA molecules targeting an HPFH region. Triangles represent the on-target site while open circles represent a potential off-target site for each guide RNA tested.

DEFINITIONS

The terms “CRISPR system,” “Cas system” or “CRISPR/Cas system” refer to a set of molecules comprising an RNA-guided nuclease or other effector molecule and a gRNA molecule that together are necessary and sufficient to direct and effect modification of nucleic acid at a target sequence by the RNA-guided nuclease or other effector molecule. In one embodiment, a CRISPR system comprises a gRNA and a Cas protein, e.g., a Cas9 protein. Such systems comprising a Cas9 or modified Cas9 molecule are referred to herein as “Cas9 systems” or “CRISPR/Cas9 systems.” In one example, the gRNA molecule and Cas molecule may be complexed, to form a ribonuclear protein (RNP) complex.

The terms “guide RNA,” “guide RNA molecule,” “gRNA molecule” or “gRNA” are used interchangeably, and refer to a set of nucleic acid molecules that promote the specific directing of a RNA-guided nuclease or other effector molecule (typically in complex with the gRNA molecule) to a target sequence. In some embodiments, said directing is accomplished through hybridization of a portion of the gRNA to DNA (e.g., through the gRNA targeting domain), and by binding of a portion of the gRNA molecule to the RNA-guided nuclease or other effector molecule (e.g., through at least the gRNA tracr). In embodiments, a gRNA molecule consists of a single contiguous polynucleotide molecule, referred to herein as a “single guide RNA” or “sgRNA” and the like. In other embodiments, a gRNA molecule consists of a plurality, usually two, polynucleotide molecules, which are themselves capable of association, usually through hybridization, referred to herein as a “dual guide RNA” or “dgRNA,” and the like. gRNA molecules are described in more detail below, but generally include a targeting domain and a tracr. In embodiments the targeting domain and tracr are disposed on a single polynucleotide. In other embodiments, the targeting domain and tracr are disposed on separate polynucleotides.

The term “targeting domain” as the term is used in connection with a gRNA, is the portion of the gRNA molecule that recognizes, e.g., is complementary to, a target sequence, e.g., a target sequence within the nucleic acid of a cell, e.g., within a gene.

The term “crRNA” as the term is used in connection with a gRNA molecule, is a portion of the gRNA molecule that comprises a targeting domain and a region that interacts with a tracr to form a flagpole region.

The term “target sequence” refers to a sequence of nucleic acids complimentary, for example fully complementary, to a gRNA targeting domain. In embodiments, the target sequence is disposed on genomic DNA. In an embodiment the target sequence is adjacent to (either on the same strand or on the complementary strand of DNA) a protospacer adjacent motif (PAM) sequence recognized by a protein having nuclease or other effector activity, e.g., a PAM sequence recognized by Cas9. In embodiments, the target sequence is a target sequence within a gene or locus that affects expression of a globin gene, e.g., that affects expression of beta globin or fetal hemoglobin (HbF). In embodiments, the target sequence is a target sequence within the globin locus. In embodiments, the target sequence is a target sequence within the BCL11a gene. In embodiments, the target sequence is a target sequence within the BCL11a enhancer region. In embodiments, the target sequence is a target sequence within a HPFH region.

The term “flagpole” as used herein in connection with a gRNA molecule, refers to the portion of the gRNA where the crRNA and the tracr bind to, or hybridize to, one another.

The term “tracr” as used herein in connection with a gRNA molecule, refers to the portion of the gRNA that binds to a nuclease or other effector molecule. In embodiments, the tracr comprises nucleic acid sequence that binds specifically to Cas9. In embodiments, the tracr comprises nucleic acid sequence that forms part of the flagpole.

The terms “Cas9” or “Cas9 molecule” refer to an enzyme from bacterial Type II CRISPR/Cas system responsible for DNA cleavage. Cas9 also includes wild-type protein as well as functional and non-functional mutants thereof. In embodiments, the Cas9 is a Cas9 of S. pyogenes.

The term “complementary” as used in connection with nucleic acid, refers to the pairing of bases, A with T or U, and G with C. The term complementary refers to nucleic acid molecules that are completely complementary, that is, form A to T or U pairs and G to C pairs across the entire reference sequence, as well as molecules that are at least 80%, 85%, 90%, 95%, 99% complementary.

“Template Nucleic Acid” as used in connection with homology-directed repair or homologous recombination, refers to nucleic acid to be inserted at the site of modification by the CRISPR system donor sequence for gene repair (insertion) at site of cutting.

An “indel,” as the term is used herein, refers to a nucleic acid comprising one or more insertions of nucleotides, one or more deletions of nucleotides, or a combination of insertions and delections of nucleotides, relative to a reference nucleic acid, that results after being exposed to a composition comprising a gRNA molecule, for example a CRISPR system. Indels can be determined by sequencing nucleic acid after being exposed to a composition comprising a gRNA molecule, for example, by NGS. With respect to the site of an indel, an indel is said to be “at or near” a reference site (e.g., a site complementary to a targeting domain of a gRNA molecule) if it comprises at least one insertion or deletion within about 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 nucleotide(s) of the reference site, or is overlapping with part or all of said reference site (e.g., comprises at least one insertion or deletion overlapping with, or within 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 nucleotides of a site complementary to the targeting domain of a gRNA molecule, e.g., a gRNA molecule described herein).

An “indel pattern,” as the term is used herein, refers to a set of indels that results after exposure to a composition comprising a gRNA molecule. In an embodiment, the indel pattern consists of the top three indels, by frequency of appearance. In an embodiment, the indel pattern consists of the top five indels, by frequency of appearance. In an embodiment, the indel pattern consists of the indels which are present at greater than about 5% frequency relative to all sequencing reads. In an embodiment, the indel pattern consists of the indels which are present at greater than about 10% frequency relative to to total number of indel sequencing reads (i.e., those reads that do not consist of the unmodified reference nucleic acid sequence). In an embodiment, the indel pattern includes of any 3 of the top five most frequently observed indels. The indel pattern may be determined, for example, by sequencing cells of a population of cells which were exposed to the gRNA molecule.

An “off-target indel,” as the term I used herein, refers to an indel at or near a site other than the target sequence of the targeting domain of the gRNA molecule. Such sites may comprise, for example, 1, 2, 3, 4, 5 or more mismatch nucleotides relative to the sequence of the targeting domain of the gRNA. In exemplary embodiments, such sites are detected using targeted sequencing of in silico predicted off-target sites, or by an insertional method known in the art.

The term “a” and “an” refers to one or to more than one (i.e., to at least one) of the grammatical object of the article. By way of example, “an element” means one element or more than one element.

The term “about” when referring to a measurable value such as an amount, a temporal duration, and the like, is meant to encompass variations of ±20% or in some instances ±10%, or in some instances ±5%, or in some instances ±1%, or in some instances ±0.1% from the specified value, as such variations are appropriate to perform the disclosed methods.

The term “antigen” or “Ag” refers to a molecule that provokes an immune response. This immune response may involve either antibody production, or the activation of specific immunologically-competent cells, or both. The skilled artisan will understand that any macromolecule, including virtually all proteins or peptides, can serve as an antigen. Furthermore, antigens can be derived from recombinant or genomic DNA. A skilled artisan will understand that any DNA, which comprises a nucleotide sequences or a partial nucleotide sequence encoding a protein that elicits an immune response therefore encodes an “antigen” as that term is used herein. Furthermore, one skilled in the art will understand that an antigen need not be encoded solely by a full length nucleotide sequence of a gene. It is readily apparent that the present invention includes, but is not limited to, the use of partial nucleotide sequences of more than one gene and that these nucleotide sequences are arranged in various combinations to encode polypeptides that elicit the desired immune response. Moreover, a skilled artisan will understand that an antigen need not be encoded by a “gene” at all. It is readily apparent that an antigen can be synthesized or can be derived from a biological sample, or might be macromolecule besides a polypeptide. Such a biological sample can include, but is not limited to a tissue sample, a cell or a fluid with other biological components.

The term “autologous” refers to any material derived from the same individual into whom it is later to be re-introduced.

The term “allogeneic” refers to any material derived from a different animal of the same species as the individual to whom the material is introduced. Two or more individuals are said to be allogeneic to one another when the genes at one or more loci are not identical. In some aspects, allogeneic material from individuals of the same species may be sufficiently unlike genetically to interact antigenically

The term “xenogeneic” refers to a graft derived from an animal of a different species.

“Derived from” as that term is used herein, indicates a relationship between a first and a second molecule. It generally refers to structural similarity between the first molecule and a second molecule and does not connotate or include a process or source limitation on a first molecule that is derived from a second molecule.

The term “encoding” refers to the inherent property of specific sequences of nucleotides in a polynucleotide, such as a gene, a cDNA, or an mRNA, to serve as templates for synthesis of other polymers and macromolecules in biological processes having either a defined sequence of nucleotides (e.g., rRNA, tRNA and mRNA) or a defined sequence of amino acids and the biological properties resulting therefrom. Thus, a gene, cDNA, or RNA, encodes a protein if transcription and translation of mRNA corresponding to that gene produces the protein in a cell or other biological system. Both the coding strand, the nucleotide sequence of which is identical to the mRNA sequence and is usually provided in sequence listings, and the non-coding strand, used as the template for transcription of a gene or cDNA, can be referred to as encoding the protein or other product of that gene or cDNA.

Unless otherwise specified, a “nucleotide sequence encoding an amino acid sequence” includes all nucleotide sequences that are degenerate versions of each other and that encode the same amino acid sequence. The phrase nucleotide sequence that encodes a protein or a RNA may also include introns to the extent that the nucleotide sequence encoding the protein may in some version contain an intron(s).

The term “effective amount” or “therapeutically effective amount” are used interchangeably herein, and refer to an amount of a compound, formulation, material, or composition, as described herein effective to achieve a particular biological result.

The term “endogenous” refers to any material from or produced inside an organism, cell, tissue or system.

The term “exogenous” refers to any material introduced from or produced outside an organism, cell, tissue or system.

The term “expression” refers to the transcription and/or translation of a particular nucleotide sequence driven by a promoter.

The term “transfer vector” refers to a composition of matter which comprises an isolated nucleic acid and which can be used to deliver the isolated nucleic acid to the interior of a cell. Numerous vectors are known in the art including, but not limited to, linear polynucleotides, polynucleotides associated with ionic or amphiphilic compounds, plasmids, and viruses. Thus, the term “transfer vector” includes an autonomously replicating plasmid or a virus. The term should also be construed to further include non-plasmid and non-viral compounds which facilitate transfer of nucleic acid into cells, such as, for example, a polylysine compound, liposome, and the like. Examples of viral transfer vectors include, but are not limited to, adenoviral vectors, adeno-associated virus vectors, retroviral vectors, lentiviral vectors, and the like.

The term “expression vector” refers to a vector comprising a recombinant polynucleotide comprising expression control sequences operatively linked to a nucleotide sequence to be expressed. An expression vector comprises sufficient cis-acting elements for expression; other elements for expression can be supplied by the host cell or in an in vitro expression system. Expression vectors include all those known in the art, including cosmids, plasmids (e.g., naked or contained in liposomes) and viruses (e.g., lentiviruses, retroviruses, adenoviruses, and adeno-associated viruses) that incorporate the recombinant polynucleotide.

The term “homologous” or “identity” refers to the subunit sequence identity between two polymeric molecules, e.g., between two nucleic acid molecules, such as, two DNA molecules or two RNA molecules, or between two polypeptide molecules. When a subunit position in both of the two molecules is occupied by the same monomeric subunit; e.g., if a position in each of two DNA molecules is occupied by adenine, then they are homologous or identical at that position. The homology between two sequences is a direct function of the number of matching or homologous positions; e.g., if half (e.g., five positions in a polymer ten subunits in length) of the positions in two sequences are homologous, the two sequences are 50% homologous; if 90% of the positions (e.g., 9 of 10), are matched or homologous, the two sequences are 90% homologous.

The term “isolated” means altered or removed from the natural state. For example, a nucleic acid or a peptide naturally present in a living animal is not “isolated,” but the same nucleic acid or peptide partially or completely separated from the coexisting materials of its natural state is “isolated.” An isolated nucleic acid or protein can exist in substantially purified form, or can exist in a non-native environment such as, for example, a host cell.

The term “operably linked” or “transcriptional control” refers to functional linkage between a regulatory sequence and a heterologous nucleic acid sequence resulting in expression of the latter. For example, a first nucleic acid sequence is operably linked with a second nucleic acid sequence when the first nucleic acid sequence is placed in a functional relationship with the second nucleic acid sequence. For instance, a promoter is operably linked to a coding sequence if the promoter affects the transcription or expression of the coding sequence. Operably linked DNA sequences can be contiguous with each other and, e.g., where necessary to join two protein coding regions, are in the same reading frame.

The term “parenteral” administration of an immunogenic composition includes, e.g., subcutaneous (s.c.), intravenous (i.v.), intramuscular (i.m.), or infrasternal injection, intratumoral, or infusion techniques.

The term “nucleic acid” or “polynucleotide” refers to deoxyribonucleic acids (DNA) or ribonucleic acids (RNA) and polymers thereof in either single- or double-stranded form. Unless specifically limited, the term encompasses nucleic acids containing known analogues of natural nucleotides that have similar binding properties as the reference nucleic acid and are metabolized in a manner similar to naturally occurring nucleotides. Unless otherwise indicated, a particular nucleic acid sequence also implicitly encompasses conservatively modified variants thereof (e.g., degenerate codon substitutions), alleles, orthologs, SNPs, and complementary sequences as well as the sequence explicitly indicated. Specifically, degenerate codon substitutions may be achieved by generating sequences in which the third position of one or more selected (or all) codons is substituted with mixed-base and/or deoxyinosine residues (Batzer et al., Nucleic Acid Res. 19:5081 (1991); Ohtsuka et al., J. Biol. Chem. 260:2605-2608 (1985); and Rossolini et al., Mol. Cell. Probes 8:91-98 (1994)).

The terms “peptide,” “polypeptide,” and “protein” are used interchangeably, and refer to a compound comprised of amino acid residues covalently linked by peptide bonds. A protein or peptide must contain at least two amino acids, and no limitation is placed on the maximum number of amino acids that can comprise a protein's or peptide's sequence. Polypeptides include any peptide or protein comprising two or more amino acids joined to each other by peptide bonds. As used herein, the term refers to both short chains, which also commonly are referred to in the art as peptides, oligopeptides and oligomers, for example, and to longer chains, which generally are referred to in the art as proteins, of which there are many types. “Polypeptides” include, for example, biologically active fragments, substantially homologous polypeptides, oligopeptides, homodimers, heterodimers, variants of polypeptides, modified polypeptides, derivatives, analogs, fusion proteins, among others. A polypeptide includes a natural peptide, a recombinant peptide, or a combination thereof.

The term “promoter” refers to a DNA sequence recognized by the synthetic machinery of the cell, or introduced synthetic machinery, required to initiate the specific transcription of a polynucleotide sequence.

The term “promoter/regulatory sequence” refers to a nucleic acid sequence which is required for expression of a gene product operably linked to the promoter/regulatory sequence. In some instances, this sequence may be the core promoter sequence and in other instances, this sequence may also include an enhancer sequence and other regulatory elements which are required for expression of the gene product. The promoter/regulatory sequence may, for example, be one which expresses the gene product in a tissue specific manner.

The term “constitutive” promoter refers to a nucleotide sequence which, when operably linked with a polynucleotide which encodes or specifies a gene product, causes the gene product to be produced in a cell under most or all physiological conditions of the cell.

The term “inducible” promoter refers to a nucleotide sequence which, when operably linked with a polynucleotide which encodes or specifies a gene product, causes the gene product to be produced in a cell substantially only when an inducer which corresponds to the promoter is present in the cell.

The term “tissue-specific” promoter refers to a nucleotide sequence which, when operably linked with a polynucleotide encodes or specified by a gene, causes the gene product to be produced in a cell substantially only if the cell is a cell of the tissue type corresponding to the promoter.

As used herein in connection with a messenger RNA (mRNA), a 5′ cap (also termed an RNA cap, an RNA 7-methylguanosine cap or an RNA m7G cap) is a modified guanine nucleotide that has been added to the “front” or 5′ end of a eukaryotic messenger RNA shortly after the start of transcription. The 5′ cap consists of a terminal group which is linked to the first transcribed nucleotide. Its presence is critical for recognition by the ribosome and protection from RNases. Cap addition is coupled to transcription, and occurs co-transcriptionally, such that each influences the other. Shortly after the start of transcription, the 5′ end of the mRNA being synthesized is bound by a cap-synthesizing complex associated with RNA polymerase. This enzymatic complex catalyzes the chemical reactions that are required for mRNA capping. Synthesis proceeds as a multi-step biochemical reaction. The capping moiety can be modified to modulate functionality of mRNA such as its stability or efficiency of translation.

As used herein, “in vitro transcribed RNA” refers to RNA, preferably mRNA, that has been synthesized in vitro. Generally, the in vitro transcribed RNA is generated from an in vitro transcription vector. The in vitro transcription vector comprises a template that is used to generate the in vitro transcribed RNA.

As used herein, a “poly(A)” is a series of adenosines attached by polyadenylation to the mRNA. In the preferred embodiment of a construct for transient expression, the polyA is between 50 and 5000 (SEQ ID NO: 6596), preferably greater than 64, more preferably greater than 100, most preferably greater than 300 or 400. poly(A) sequences can be modified chemically or enzymatically to modulate mRNA functionality such as localization, stability or efficiency of translation.

As used herein, “polyadenylation” refers to the covalent linkage of a polyadenylyl moiety, or its modified variant, to a messenger RNA molecule. In eukaryotic organisms, most messenger RNA (mRNA) molecules are polyadenylated at the 3′ end. The 3′ poly(A) tail is a long sequence of adenine nucleotides (often several hundred) added to the pre-mRNA through the action of an enzyme, polyadenylate polymerase. In higher eukaryotes, the poly(A) tail is added onto transcripts that contain a specific sequence, the polyadenylation signal. The poly(A) tail and the protein bound to it aid in protecting mRNA from degradation by exonucleases. Polyadenylation is also important for transcription termination, export of the mRNA from the nucleus, and translation. Polyadenylation occurs in the nucleus immediately after transcription of DNA into RNA, but additionally can also occur later in the cytoplasm. After transcription has been terminated, the mRNA chain is cleaved through the action of an endonuclease complex associated with RNA polymerase. The cleavage site is usually characterized by the presence of the base sequence AAUAAA near the cleavage site. After the mRNA has been cleaved, adenosine residues are added to the free 3′ end at the cleavage site.

As used herein, “transient” refers to expression of a non-integrated transgene for a period of hours, days or weeks, wherein the period of time of expression is less than the period of time for expression of the gene if integrated into the genome or contained within a stable plasmid replicon in the host cell.

As used herein, the terms “treat”, “treatment” and “treating” refer to the reduction or amelioration of the progression, severity and/or duration of a disorder, e.g., a hemoglobinopathy, or the amelioration of one or more symptoms (preferably, one or more discernible symptoms) of a disorder, e.g., a hemoglobinopathy, resulting from the administration of one or more therapies (e.g., one or more therapeutic agents such as a gRNA molecule, CRISPR system, or modified cell of the invention). In specific embodiments, the terms “treat”, “treatment” and “treating” refer to the amelioration of at least one measurable physical parameter of a hemoglobinopathy disorder, not discernible by the patient. In other embodiments the terms “treat”, “treatment” and “treating” refer to the inhibition of the progression of a disorder, either physically by, e.g., stabilization of a discernible symptom, physiologically by, e.g., stabilization of a physical parameter, or both. In other embodiments the terms “treat”, “treatment” and “treating” refer to the reduction or stabilization of a symptom of a hemoglobinopathy, e.g., sickle cell disease or beta-thalassemia.

The term “signal transduction pathway” refers to the biochemical relationship between a variety of signal transduction molecules that play a role in the transmission of a signal from one portion of a cell to another portion of a cell. The phrase “cell surface receptor” includes molecules and complexes of molecules capable of receiving a signal and transmitting signal across the membrane of a cell.

The term “subject” is intended to include living organisms in which an immune response can be elicited (e.g., mammals, human).

The term, a “substantially purified” cell refers to a cell that is essentially free of other cell types. A substantially purified cell also refers to a cell which has been separated from other cell types with which it is normally associated in its naturally occurring state. In some instances, a population of substantially purified cells refers to a homogenous population of cells. In other instances, this term refers simply to cell that have been separated from the cells with which they are naturally associated in their natural state. In some aspects, the cells are cultured in vitro. In other aspects, the cells are not cultured in vitro.

The term “therapeutic” as used herein means a treatment. A therapeutic effect is obtained by reduction, suppression, remission, or eradication of a disease state.

The term “prophylaxis” as used herein means the prevention of or protective treatment for a disease or disease state.

The term “transfected” or “transformed” or “transduced” refers to a process by which exogenous nucleic acid and/or protein is transferred or introduced into the host cell. A “transfected” or “transformed” or “transduced” cell is one which has been transfected, transformed or transduced with exogenous nucleic acid and/or protein. The cell includes the primary subject cell and its progeny.

The term “specifically binds,” refers to a molecule recognizing and binding with a binding partner (e.g., a protein or nucleic acid) present in a sample, but which molecule does not substantially recognize or bind other molecules in the sample.

The term “bioequivalent” refers to an amount of an agent other than the reference compound, required to produce an effect equivalent to the effect produced by the reference dose or reference amount of the reference compound.

“Refractory” as used herein refers to a disease, e.g., a hemoglobinopathy, that does not respond to a treatment. In embodiments, a refractory hemoglobinopathy can be resistant to a treatment before or at the beginning of the treatment. In other embodiments, the refractory hemoglobinopathy can become resistant during a treatment. A refractory hemoglobinopathy is also called a resistant hemoglobinopathy.

“Relapsed” as used herein refers to the return of a disease (e.g., hemoglobinopathy) or the signs and symptoms of a disease such as a hemoglobinopathy after a period of improvement, e.g., after prior treatment of a therapy, e.g., hemoglobinopathy therapy.

Ranges: throughout this disclosure, various aspects of the invention can be presented in a range format. It should be understood that the description in range format is merely for convenience and brevity and should not be construed as an inflexible limitation on the scope of the invention. Accordingly, the description of a range should be considered to have specifically disclosed all the possible subranges as well as individual numerical values within that range. For example, description of a range such as from 1 to 6 should be considered to have specifically disclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numbers within that range, for example, 1, 2, 2.7, 3, 4, 5, 5.3, and 6. As another example, a range such as 95-99% identity, includes something with 95%, 96%, 97%, 98% or 99% identity, and includes subranges such as 96-99%, 96-98%, 96-97%, 97-99%, 97-98% and 98-99% identity. This applies regardless of the breadth of the range.

The term “BCL11a” refers to B-cell lymphoma/leukemia 11A, a RNA polymerase II core promoter proximal region sequence-specific DNA binding protein, and the gene encoding said protein, together with all introns and exons. This gene encodes a C2H2 type zinc-finger protein. BCL11A has been found to play a role in the suppression of fetal hemoglobin production. BCL11a is also known as B-Cell CLL/Lymphoma 11A (Zinc Finger Protein), CTIP1, EVI9, Ecotropic Viral Integration Site 9 Protein Homolog, COUP-TF-Interacting Protein 1, Zinc Finger Protein 856, KIAA1809, BCL-11A, ZNF856, EVI-9, and B-Cell CLL/Lymphoma 11A. The term encompasses all isoforms and splice variants of BLC11a. The human gene encoding BCL11a is mapped to chromosomal location 2p16.1 (by Ensembl). The human and murine amino acid and nucleic acid sequences can be found in a public database, such as GenBank, UniProt and Swiss-Prot., and the genomic sequence of human BCL11a can be found in GenBank at NC_000002.12. The BCL11a gene refers to this genomic location, including all introns and exons. There are multiple known isotypes of BCL11a.

The sequence of mRNA encoding isoform 1 of human BCL11a can be found at NM_022893.

The peptide sequence of isoform 1 of human BCL11a is:

        10         20         30         40 MSRRKQGKPQ HLSKREFSPE PLEAILTDDE PDHGPLGAPE         50         60         70         80 GDHDLLTCGQ CQMNFPLGDI LIFIEHKRKQ CNGSLCLEKA         90        100        110        120 VDKPPSPSPI EMKKASNPVE VGIQVTPEDD DCLSTSSRGI        130        140        150        160 CPKQEHIADK LLHWRGLSSP RSAHGALIPT PGMSAEYAPQ        170        180        190        200 GICKDEPSSY TCTTCKQPFT SAWFLLQHAQ NTHGLRIYLE        210        220        230        240 SEHGSPLTPR VGIPSGLGAE CPSQPPLHGI HIADNNPFNL        250        260        270        280 LRIPGSVSRE ASGLAEGRFP PTPPLFSPPP RHHLDPHRIE        290        300        310        320 RLGAEEMALA THHPSAFDRV LRLNPMAMEP PAMDFSRRLR        330        340        350        360 ELAGNTSSPP LSPGRPSPMQ RLLQPFQPGS KPPFLATPPL        370        380        390        400 PPLQSAPPPS QPPVKSKSCE FCGKTFKFQS NLVVHRRSHT        410        420        430        440 GEKPYKCNLC DHACTQASKL KRHMKTHMHK SSPMTVKSDD        450        460        470        480 GLSTASSPEP GTSDLVGSAS SALKSVVAKF KSENDPNLIP        490        500        510        520 ENGDEEEEED DEEEEEEEEE EEEELTESER VDYGFGLSLE        530        540        550        560 AARHHENSSR GAVVGVGDES RALPDVMQGM VLSSMQHFSE        570        580        590        600 AFHQVLGEKH KRGHLAEAEG HRDTCDEDSV AGESDRIDDG        610        620        630        640 TVNGRGCSPG ESASGGLSKK LLLGSPSSLS PFSKRIKLEK        650        660        670        680 EFDLPPAAMP NTENVYSQWL AGYAASRQLK DPFLSFGDSR        690        700        710        720 QSPFASSSEH SSENGSLRFS TPPGELDGGI SGRSGTGSGG        730        740        750        760 STPHISGPGP GRPSSKEGRR SDTCEYCGKV FKNCSNLTVH        770        780        790        800 RRSHTGERPY KCELCNYACA QSSKLTRHMK THGQVGKDVY        810        820        830 KCEICKMPFS VYSTLEKHMK KWHSDRVLNN DIKTE

SEQ ID NO: 21-1 (Identifier Q9H165-1; and NM_022893.3; and accession ADL14508.1).

The sequences of other BCL11a protein isoforms are provided at:

Isoform 2: Q9H165-2 Isoform 3: Q9H165-3 Isoform 4: Q9H165-4 Isoform 5: Q9H165-5 Isoform 6: Q9H165-6

As used herein, a human BCL11a protein also encompasses proteins that have over its full length at least about 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity with BCL11a isolorm 1-6, wherein such proteins still have at least one of the functions of BCL11a.

The term “globin locus” as used herein refers to the region of human chromosome 11 comprising genes for embryonic (ε), fetal (G(γ) and A(γ)), adult globin genes (γ and β), locus control regions and DNase I hypersensitivity sites.

The term “complementary” as used in connection with nucleic acid, refers to the pairing of bases, A with T or U, and G with C. The term complementary refers to nucleic acid molecules that are completely complementary, that is, form A to T or U pairs and G to C pairs across the entire reference sequence, as well as molecules that are at least 80%, 85%, 90%, 95%, 99% complementary.

The term “HPFH” refers to hereditary persistence of fetal hemoglobin, and is characterized in increased fetal hemoglobin in adult red blood cells. The term “HPFH region” refers to a genomic site which, when modified (e.g., mutated or deleted), causes increased HbF production in adult red blood cells, and includes HPFH sites identified in the literature (see e.g., the Online Mendelian Inheritance in Man: http://www.omim.org/entry/141749). In an exemplary embodiment, the HPFH region is a region within or encompassing the beta globin gene cluster on chromosome 11p15. In an exemplary embodiment, the HPFH region is within or emcompasses at least part of the delta globin gene. In an exemplary embodiment, the HPFH region is a region of the promoter of HBG1. In an exemplary embodiment, the HPFH region is a region of the promoter of HBG1. In an exemplary embodiment, the HPFH region is a region described in Sankaran V G et al. NEJM (2011) 365:807-814. In an exemplary embodiment, the HPFH region is the French breakpoint deletional HPFH as described in Sankaran V G et al. NEJM (2011) 365:807-814. In an exemplary embodiment, the HPFH region is the Algerian HPFH as described in Sankaran V G et al. NEJM (2011) 365:807-814. In an exemplary embodiment, the HPFH region is the Sri Lankan HPFH as described in Sankaran V G et al. NEJM (2011) 365:807-814. In an exemplary embodiment, the HPFH region is the HPFH-3 as described in Sankaran V G et al. NEJM (2011) 365:807-814. In an exemplary embodiment, the HPFH region is the HPFH-2 as described in Sankaran V G et al. NEJM (2011) 365:807-814. In an embodiment, the HPFH-1 region is the HPFH-3 as described in Sankaran V G et al. NEJM (2011) 365:807-814. In an exemplary embodiment, the HPFH region is the Sri Lankan (δβ)⁰-thalassemia HPFH as described in Sankaran V G et al. NEJM (2011) 365:807-814. In an exemplary embodiment, the HPFH region is the Sicilian (δβ)⁰-thalassemia HPFH as described in Sankaran V G et al. NEJM (2011) 365:807-814. In an exemplary embodiment, the HPFH region is the Macedonian (δβ)⁰-thalassemia HPFH as described in Sankaran V G et al. NEJM (2011) 365:807-814. In an exemplary embodiment, the HPFH region is the Kurdish β⁰-thalassemia HPFH as described in Sankaran V G et al. NEJM (2011) 365:807-814. In an exemplary embodiment, the HPFH region is the region located at Chr11:5213874-5214400 (hg18). In an exemplary embodiment, the HPFH region is the region located at Chr11:5215943-5215046 (hg18). In an exemplary embodiment, the HPFH region is the region located at Chr11:5234390-5238486 (hg38).

“BCL11a enhancer” as the term is used herein, refers to nucleic acid sequence which affects, e.g., enhances, expression or function of BCL11a. See e.g., Bauer et al., Science, vol. 342, 2013, pp. 253-257. The BCL11a enhancer may be, for example, operative only in certain cell types, for example, cells of the erythroid lineage. One example of a BCL11a enhancer is the nucleic acid sequence between exon 2 and exon 3 of the BCL11a gene gene (e.g., the nucleic acid at or corresponding to positions +55: Chr2:60497676-60498941; +58: Chr2:60494251-60495546; +62: Chr2:60490409-60491734 as recorded in hg38). In an embodiment, the BCL11a Enhancer is the +62 region of the nucleic acid sequence between exon 2 and exon 3 of the BCL11a gene. In an embodiment, the BCL11a Enhancer is the +58 region of the nucleic acid sequence between exon 2 and exon 3 of the BCL11a gene. In an embodiment, the BCL11a Enhancer is the +55 region of the nucleic acid sequence between exon 2 and exon 3 of the BCL11a gene.

The terms “hematopoietic stem and progenitor cell” or “HSPC” are used interchangeably, and refer to a population of cells comprising both hematopoietic stem cells (“HSCs”) and hematopoietic progenitor cells (“HPCs”). Such cells are characterized, for example, as CD34+. In exemplary embodiments, HSPCs are isolated from bone marrow. In other exemplary embodiments, HSPCs are isolated from peripheral blood. In other exemplary embodiments, HSPCs are isolated from umbilical cord blood.

“Stem cell expander” as used herein refers to a compound which causes cells, e.g., HSPCs, HSCs and/or HPCs to proliferate, e.g., increase in number, at a faster rate relative to the same cell types absent said agent. In one exemplary aspect, the stem cell expander is an inhibitor of the aryl hydrocarbon receptor pathway. Additional examples of stem cell expanders are provided below. In embodiments, the proliferation, e.g., increase in number, is accomplished ex vivo.

“Engraftment” or “engraft” refers to the incorporation of a cell or tissue, e.g., a population of HSPCs, into the body of a recipient, e.g., a mammal or human subject. In one example, engraftment includes the growth, expansion and/or differention of the engrafted cells in the recipient. In an example, engraftment of HSPCs includes the differentiation and growth of said HSPCs into erythroid cells within the body of the recipient.

The term “Hematopoietic progenitor cells” (HPCs) as used herein refers to primitive hematopoietic cells that have a limited capacity for self-renewal and the potential for multilineage differentiation (e.g., myeloid, lymphoid), mono-lineage differentiation (e.g., myeloid or lymphoid) or cell-type restricted differentiation (e.g., erythroid progenitor) depending on placement within the hematopoietic hierarchy (Doulatov et al., Cell Stem Cell 2012).

“Hematopoietic stem cells” (HSCs) as used herein refer to immature blood cells having the capacity to self-renew and to differentiate into more mature blood cells comprising granulocytes (e.g., promyelocytes, neutrophils, eosinophils, basophils), erythrocytes (e.g., reticulocytes, erythrocytes), thrombocytes (e.g., megakaryoblasts, platelet producing megakaryocytes, platelets), and monocytes (e.g., monocytes, macrophages). HSCs are interchangeably described as stem cells throughout the specification. It is known in the art that such cells may or may not include CD34+ cells. CD34+ cells are immature cells that express the CD34 cell surface marker. CD34+ cells are believed to include a subpopulation of cells with the stem cell properties defined above. It is well known in the art that HSCs are multipotent cells that can give rise to primitive progenitor cells (e.g., multipotent progenitor cells) and/or progenitor cells committed to specific hematopoietic lineages (e.g., lymphoid progenitor cells). The stem cells committed to specific hematopoietic lineages may be of T cell lineage, B cell lineage, dendritic cell lineage, Langerhans cell lineage and/or lymphoid tissue-specific macrophage cell lineage. In addition, HSCs also refer to long term HSC (LT-HSC) and short term HSC (ST-HSC). ST-HSCs are more active and more proliferative than LT-HSCs. However, LT-HSC have unlimited self renewal (i.e., they survive throughout adulthood), whereas ST-HSC have limited self renewal (i.e., they survive for only a limited period of time). Any of these HSCs can be used in any of the methods described herein. Optionally, ST-HSCs are useful because they are highly proliferative and thus, quickly increase the number of HSCs and their progeny. Hematopoietic stem cells are optionally obtained from blood products. A blood product includes a product obtained from the body or an organ of the body containing cells of hematopoietic origin. Such sources include un-fractionated bone marrow, umbilical cord, peripheral blood (e.g., mobilized peripheral blood, e.g., moblized with a mobilization agent such as G-CSF or Plerixafor® (AMD3100)), liver, thymus, lymph and spleen. All of the aforementioned crude or un-fractionated blood products can be enriched for cells having hematopoietic stem cell characteristics in ways known to those of skill in the art. In an embodiment, HSCs are characterized as CD34+/CD38−/CD90+/CD45RA−. In embodiments, the HSC s are characterized as CD34+/CD90+/CD49f+ cells.

“Expansion” or “Expand” in the context of cells refers to an increase in the number of a characteristic cell type, or cell types, from an initial cell population of cells, which may or may not be identical. The initial cells used for expansion may not be the same as the cells generated from expansion.

“Cell population” refers to eukaryotic mammalian, preferably human, cells isolated from biological sources, for example, blood product or tissues and derived from more than one cell.

“Enriched” when used in the context of cell population refers to a cell population selected based on the presence of one or more markers, for example, CD34+.

The term “CD34+ cells” refers to cells that express at their surface CD34 marker. CD34+ cells can be detected and counted using for example flow cytometry and fluorescently labeled anti-CD34 antibodies.

“Enriched in CD34+ cells” means that a cell population has been selected based on the presence of CD34 marker. Accordingly, the percentage of CD34+ cells in the cell population after selection method is higher than the percentage of CD34+ cells in the initial cell population before selecting step based on CD34 markers. For example, CD34+ cells may represent at least 50%, 60%, 70%, 80% or at least 90% of the cells in a cell population enriched in CD34+ cells.

The terms “F cell” and “F-cell” refer to cells, usually erythrocytes (e.g., red blood cells) which contain and/or produce (e.g., express) fetal hemoglobin. For example, an F-cell is a cell that contains or produces detectible levels of fetal hemoglobin. For example, an F-cell is a cell that contains or produces at least 5 picograms of fetal hemoglobin. In another example, an F-cell is a cell that contains or produces at least 6 picograms of fetal hemoglobin. In another example, an F-cell is a cell that contains or produces at least 7 picograms of fetal hemoglobin. In another example, an F-cell is a cell that contains or produces at least 8 picograms of fetal hemoglobin. In another example, an F-cell is a cell that contains or produces at least 9 picograms of fetal hemoglobin. In another example, an F-cell is a cell that contains or produces at least 10 picograms of fetal hemoglobin. Levels of fetal hemoglobin may be measured using an assay described herein or by other method known in the art, for example, flow cytometry using an anti-fetal hemoglobin detection reagent, high performance liquid chromatography, mass spectrometry, or enzyme-linked immunoabsorbent assay.

Unless otherwise stated, all genome or chromosome coordinates are are according to hg38.

DETAILED DESCRIPTION

The gRNA molecules, compositions and methods described herein relate to genome editing in eukaryotic cells using the CRISPR/Cas9 system. In particular, the gRNA molecules, compositions and methods described herein relate to regulation of globin levels and are useful, for example, in regulating expression and production of globin genes and protein. The gRNA molecules, compositions and methods can be useful in the treatment of hemoglobinopathies.

I. 2RNA Molecules

A gRNA molecule may have a number of domains, as described more fully below, however, a gRNA molecule typically comprises at least a crRNA domain (comprising a targeting domain) and a tracr. The gRNA molecules of the invention, used as a component of a CRISPR system, are useful for modifying (e.g., modifying the sequence) DNA at or near a target site. Such modifications include deletions and or insertions that result in, for example, reduced or eliminated expression of a functional product of the gene comprising the target site. These uses, and additional uses, are described more fully below.

In an embodiment, a unimolecular, or sgRNA comprises, preferably from 5′ to 3′: a crRNA (which contains a targeting domain complementary to a target sequence and a region that forms part of a flagpole (i.e., a crRNA flagpole region)); a loop; and a tracr (which contains a domain complementary to the crRNA flagpole region, and a domain which additionally binds a nuclease or other effector molecule, e.g., a Cas molecule, e.g., aCas9 molecule), and may take the following format (from 5′ to 3′):

[targeting domain]-[crRNA flagpole region]-[optional first flagpole extension]-[loop]-[optional first tracr extension]-[tracr flagpole region]-[tracr nuclease binding domain]

In embodiments, the tracr nuclease binding domain binds to a Cas protein, e.g., a Cas9 protein.

In an embodiment, a bimolecular, or dgRNA comprises two polynucleotides; the first, preferably from 5′ to 3′: a crRNA (which contains a targeting domain complementary to a target sequence and a region that forms part of a flagpole; and the second, preferrably from 5′ to 3′: a tracr (which contains a domain complementary to the crRNA flagpole region, and a domain which additionally binds a nuclease or other effector molecule, e.g., a Cas molecule, e.g., Cas9 molecule), and may take the following format (from 5′ to 3′):

Polynucleotide 1 (crRNA): [targeting domain]-[crRNA flagpole region]-[optional first flagpole extension]-[optional second flagpole extension] Polynucleotide 2 (tracr): [optional first tracr extension]-[tracr flagpole region]-[tracr nuclease binding domain]

In embodiments, the tracr nuclease binding domain binds to a Cas protein, e.g., a Cas9 protein.

In some aspects, the targeting domain comprises or consists of a targeting domain sequence described herein, e.g., a targeting domain described in Table 1, 2, 3, 4, 5, or 6, or a targeting domain comprising or consisting of 17, 18, 19, 20, 21, 22, 23, 24, or 25 (preferably 20) consecutive nucleotides of a targeting domain sequence described in Table 1, 2, 3, 4, 5, or 6.

In some aspects, the flagpole, e.g., the crRNA flagpole region, comprises, from 5′ to 3′: GUUUUAGAGCUA (SEQ ID NO: 6584).

In some aspects, the flagpole, e.g., the crRNA flagpole region, comprises, from 5′ to 3′: GUUUAAGAGCUA (SEQ ID NO: 6585).

In some aspects the loop comprises, from 5′ to 3′: GAAA (SEQ ID NO: 6588).

In some aspects the tracr comprises, from 5′ to 3′: UAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGG UGC (SEQ ID NO: 6589) and is preferably used in a gRNA molecule comprising SEQ ID NO 6584.

In some aspects the tracr comprises, from 5′ to 3′: UAGCAAGUUUAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGG UGC (SEQ ID NO: 6590) and is preferably used in a gRNA molecule comprising SEQ ID NO 6585.

In some aspects, the gRNA may also comprise, at the 3′ end, additional U nucleic acids. For example the gRNA may comprise an additional 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 U nucleic acids at the 3′ end. In an embodiment, the gRNA comprises an additional 4 U nucleic acids at the 3′ end. In the case of dgRNA, one or more of the polynucleotides of the dgRNA (e.g., the polynucleotide comprising the targeting domain and the polynucleotide comprising the tracr) may comprise, at the 3′ end, additional U nucleic acids. For example, the case of dgRNA, one or more of the polynucleotides of the dgRNA (e.g., the polynucleotide comprising the targeting domain and the polynucleotide comprising the tracr) may comprise an additional 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 U nucleic acids at the 3′ end. In an embodiment, in the case of dgRNA, one or more of the polynucleotides of the dgRNA (e.g., the polynucleotide comprising the targeting domain and the polynucleotide comprising the tracr) comprises an additional 4 U nucleic acids at the 3′ end. In an embodiment of a dgRNA, only the polynucleotide comprising the tracr comprises the additional U nucleic acid(s), e.g., 4 U nucleic acids. In an embodiment of a dgRNA, only the polynucleotide comprising the targeting domain comprises the additional U nucleic acid(s). In an embodiment of a dgRNA, both the polynucleotide comprising the targeting domain and the polynucleotide comprising the tracr comprise the additional U nucleic acids, e.g., 4 U nucleic acids.

In some aspects, the gRNA may also comprise, at the 3′ end, additional A nucleic acids. For example the gRNA may comprise an additional 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 A nucleic acids at the 3′ end. In an embodiment, the gRNA comprises an additional 4 A nucleic acids at the 3′ end. In the case of dgRNA, one or more of the polynucleotides of the dgRNA (e.g., the polynucleotide comprising the targeting domain and the polynucleotide comprising the tracr) may comprise, at the 3′ end, additional A nucleic acids. For example, the case of dgRNA, one or more of the polynucleotides of the dgRNA (e.g., the polynucleotide comprising the targeting domain and the polynucleotide comprising the tracr) may comprise an additional 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 A nucleic acids at the 3′ end. In an embodiment, in the case of dgRNA, one or more of the polynucleotides of the dgRNA (e.g., the polynucleotide comprising the targeting domain and the polynucleotide comprising the tracr) comprises an additional 4 A nucleic acids at the 3′ end. In an embodiment of a dgRNA, only the polynucleotide comprising the tracr comprises the additional A nucleic acid(s), e.g., 4 A nucleic acids. In an embodiment of a dgRNA, only the polynucleotide comprising the targeting domain comprises the additional A nucleic acid(s). In an embodiment of a dgRNA, both the polynucleotide comprising the targeting domain and the polynucleotide comprising the tracr comprise the additional U nucleic acids, e.g., 4 A nucleic acids.

In embodiments, one or more of the polynucleotides of the gRNA molecule may comprise a cap at the 5′ end.

In an embodiment, a unimolecular, or sgRNA comprises, preferably from 5′ to 3′: a crRNA (which contains a targeting domain complementary to a target sequence; a crRNA flagpole region; first flagpole extension; a loop; a first tracr extension (which contains a domain complementary to at least a portion of the first flagpole extension); and a tracr (which contains a domain complementary to the crRNA flagpole region, and a domain which additionally binds a Cas9 molecule). In some aspects, the targeting domain comprises a targeting domain sequence described herein, e.g., a targeting domain described in Table 1, 2, 3, 4, 5, or 6, or a targeting domain comprising or consisting of 17, 18, 19, 20, 21, 22, 23, 24, or 25 (preferably 20) consecutive nucleotides of a targeting domain sequence described in Table 1, 2, 3, 4, 5, or 6, for example the 3′ 17, 18, 19, 20, 21, 22, 23, 24 or 25 (preferably 20) consecutive nucleotides of a targeting domain sequence described in Table 1, 2, 3, 4, 5, or 6.

In aspects comprising a first flagpole extension and/or a first tracr extension, the flagpole, loop and tracr sequences may be as described above. In general any first flagpole extension and first tracr extension may be employed, provided that they are complementary. In embodiments, the first flagpole extension and first tracr extension consist of 3, 4, 5, 6, 7, 8, 9, 10 or more complementary nucleotides.

In some aspects, the first flagpole extension comprises, from 5′ to 3′: UGCUG (SEQ ID NO: 6586). In some aspects, the first flagpole extension consists of SEQ ID NO: 6586.

In some aspects, the first tracr extension comprises, from 5′ to 3′: CAGCA (SEQ ID NO: 6591). In some aspects, the first tracr extension consists of SEQ ID NO: 6591.

In an embodiment, a dgRNA comprises two nucleic acid molecules. In some aspects, the dgRNA comprises a first nucleic acid which contains, preferably from 5′ to 3′: a targeting domain complementary to a target sequence; a crRNA flagpole region; optionally a first flagpole extension; and, optionally, a second flagpole extension; and a second nucleic acid (which may be referred to herein as a tracr), and comprises at least a domain which binds a Cas molecule, e.g., a Cas9 molecule) comprising preferably from 5′ to 3′: optionally a first tracr extension; and a tracr (which contains a domain complementary to the crRNA flagpole region, and a domain which additionally binds a Cas, e.g., Cas9, molecule). The second nucleic acid may additionally comprise, at the 3′ end (e.g., 3′ to the tracr) additional U nucleic acids. For example the tracr may comprise an additional 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 U nucleic acids at the 3′ end (e.g., 3′ to the tracr). The second nucleic acid may additionally or alternately comprise, at the 3′ end (e.g., 3′ to the tracr) additional A nucleic acids. For example the tracr may comprise an additional 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 A nucleic acids at the 3′ end (e.g., 3′ to the tracr). In some aspects, the targeting domain comprises a targeting domain sequence described herein, e.g., a targeting domain described in Table 1, 2, 3, 4, 5, or 6, or a targeting domain comprising or consisting of 17, 18, 19, 20, 21, 22, 23, 24, or 25 (preferably 20) consecutive nucleotides of a targeting domain sequence described in Table 1, 2, 3, 4, 5, or 6.

In aspects involving a dgRNA, the crRNA flagpole region, optional first flagpole extension, optional first tracr extension and tracr sequences may be as described above.

In some aspects, the optional second flagpole extension comprises, from 5′ to 3′: UUUUG (SEQ ID NO: 6587).

In embodiments, the 3′ 1, 2, 3, 4, or 5 nucleotides, the 5′ 1, 2, 3, 4, or 5 nucleotides, or both the 3′ and 5′ 1, 2, 3, 4, or 5 nucleotides of the gRNA molecule (and in the case of a dgRNA molecule, the polynucleotide comprising the targeting domain and/or the polynucleotide comprising the tracr) are modified nucleic acids, as described more fully in section XIII, below.

The domains are discussed briefly below:

1) The Targeting Domain:

Guidance on the selection of targeting domains can be found, e.g., in Fu Y el al. NAT BIOTECHNOL 2014 (doi: 10.1038/nbt.2808) and Sternberg S H el al. NATURE 2014 (doi: 10.1038/nature13011).

The targeting domain comprises a nucleotide sequence that is complementary, e.g., at least 80, 85, 90, 95, or 99% complementary, e.g., fully complementary, to the target sequence on the target nucleic acid. The targeting domain is part of an RNA molecule and will therefore comprise the base uracil (U), while any DNA encoding the gRNA molecule will comprise the base thymine (T). While not wishing to be bound by theory, it is believed that the complementarity of the targeting domain with the target sequence contributes to specificity of the interaction of the gRNA molecule/Cas9 molecule complex with a target nucleic acid. It is understood that in a targeting domain and target sequence pair, the uracil bases in the targeting domain will pair with the adenine bases in the target sequence.

In an embodiment, the targeting domain is 5 to 50, e.g., 10 to 40, e.g., 10 to 30, e.g., 15 to 30, e.g., 15 to 25 nucleotides in length. In an embodiment, the targeting domain is 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 or 25 nucleotides in length. In an embodiment, the targeting domain is 16 nucleotides in length. In an embodiment, the targeting domain is 17 nucleotides in length. In an embodiment, the targeting domain is 18 nucleotides in length. In an embodiment, the targeting domain is 19 nucleotides in length. In an embodiment, the targeting domain is 20 nucleotides in length. In an embodiment, the targeting domain is 21 nucleotides in length. In an embodiment, the targeting domain is 22 nucleotides in length. In an embodiment, the targeting domain is 23 nucleotides in length. In an embodiment, the targeting domain is 24 nucleotides in length. In an embodiment, the targeting domain is 25 nucleotides in length. In embodiments, the aforementioned 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleotides comprise the 5′-16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleotides from a targeting domain described in Table 1, 2, 3, 4, 5, or 6. In embodiments, the aforementioned 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleotides comprise the 3′-16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleotides from a targeting domain described in Table 1, 2, 3, 4, 5, or 6.

Without being bound by theory, it is believed that the 8, 9, 10, 11 or 12 nucleic acids of the targeting domain disposed at the 3′ end of the targeting domain is important for targeting the target sequence, and may thus be referred to as the “core” region of the targeting domain. In an embodiment, the core domain is fully complementary with the target sequence.

The strand of the target nucleic acid with which the targeting domain is complementary is referred to herein as the target sequence. In some aspects, the target sequence is disposed on a chromosome, e.g., is a target within a gene. In some aspects the target sequence is disposed within an exon of a gene. In some aspects the target sequence is disposed within an intron of a gene. In some aspects, the target sequence comprises, or is proximal (e.g., within 10, 20, 30, 40, 50, 100, 200, 300, 400, 500, or 1000 nucleic acids) to a binding site of a regulatory element, e.g., a promoter or transcription factor binding site, of a gene of interest. Some or all of the nucleotides of the domain can have a modification, e.g., modification found in Section XIII herein.

2) crRNA Flagpole Region:

The flagpole contains portions from both the crRNA and the tracr. The crRNA flagpole region is complementary with a portion of the tracr, and in an embodiment, has sufficient complementarity to a portion of the tracr to form a duplexed region under at least some physiological conditions, for example, normal physiological conditions. In an embodiment, the crRNA flagpole region is 5 to 30 nucleotides in length. In an embodiment, the crRNA flagpole region is 5 to 25 nucleotides in length. The crRNA flagpole region can share homology with, or be derived from, a naturally occurring portion of the repeat sequence from a bacterial CRISPR array. In an embodiment, it has at least 50% homology with a crRNA flagpole region disclosed herein, e.g., an S. pyogenes, or S. thermophilus, crRNA flagpole region.

In an embodiment, the flagpole, e.g., the crRNA flagpole region, comprises SEQ ID NO: 6584. In an embodiment, the flagpole, e.g., the crRNA flagpole region, comprises sequence having at least 50%, 60%, 70%, 80%, 85%, 90%, 95% or 99% homology with SEQ ID NO: 6584. In an embodiment, the flagpole, e.g., the crRNA flagpole region, comprises at least 5, 6, 7, 8, 9, 10, or 11 nucleotides of SEQ ID NO: 6584. In an embodiment, the flagpole, e.g., the crRNA flagpole region, comprises SEQ ID NO: 6585. In an embodiment, the flagpole comprises sequence having at least 50%, 60%, 70%, 80%, 85%, 90%, 95% or 99% homology with SEQ ID NO: 6585. In an embodiment, the flagpole, e.g., the crRNA flagpole region, comprises at least 5, 6, 7, 8, 9, 10, or 11 nucleotides of SEQ ID NO: 6585.

Some or all of the nucleotides of the domain can have a modification, e.g., modification described in Section XIII herein.

3) First Flagpole Extension

When a tracr comprising a first tracr extension is used, the crRNA may comprise a first flagpole extension. In general any first flagpole extension and first tracr extension may be employed, provided that they are complementary. In embodiments, the first flagpole extension and first tracr extension consist of 3, 4, 5, 6, 7, 8, 9, 10 or more complementary nucleotides.

The first flagpole extension may comprise nucleotides that are complementary, e.g., 80%, 85%, 90%, 95% or 99%, e.g., fully complementary, with nucleotides of the first tracr extension. In some aspects, the first flagpole extension nucleotides that hybridize with complementary nucleotides of the first tracr extension are contiguous. In some aspects, the first flagpole extension nucleotides that hybridize with complementary nucleotides of the first tracr extension are discontinuous, e.g., comprises two or more regions of hybridization separated by nucleotides that do not base pair with nucleotides of the first tracr extension. In some aspects, the first flagpole extension comprises at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more nucleotides. In some aspects, the first flagpole extension comprises, from 5′ to 3′: UGCUG (SEQ ID NO: 6586). In some aspects, the first flagpole extension consists of SEQ ID NO: 6586. In some aspects the first flagpole extension comprises nucleic acid that is at least 80%, 85%, 90%, 95% or 99% homology to SEQ ID NO: 6586.

Some or all of the nucleotides of the first tracr extension can have a modification, e.g., modification found in Section XIII herein.

3) The Loop

A loop serves to link the crRNA flagpole region (or optionally the first flagpole extension, when present) with the tracr (or optionally the first tracr extension, when present) of a sgRNA. The loop can link the crRNA flagpole region and tracr covalently or non-covalently. In an embodiment, the linkage is covalent. In an embodiment, the loop covalently couples the crRNA flagpole region and tracr. In an embodiment, the loop covalently couples the first flagpole extension and the first tracr extension. In an embodiment, the loop is, or comprises, a covalent bond interposed between the crRNA flagpole region and the domain of the tracr which hybridizes to the crRNA flagpole region. Typically, the loop comprises one or more, e.g., 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides.

In dgRNA molecules the two molecules can be associated by virtue of the hybridization between at least a portion of the crRNA (e.g., the crRNA flagpole region) and at least a portion of the tracr (e.g., the domain of the tracr which is complementary to the crRNA flagpole region).

A wide variety of loops are suitable for use in sgRNAs. Loops can consist of a covalent bond, or be as short as one or a few nucleotides, e.g., 1, 2, 3, 4, or 5 nucleotides in length. In an embodiment, a loop is 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 or more nucleotides in length. In an embodiment, a loop is 2 to 50, 2 to 40, 2 to 30, 2 to 20, 2 to 10, or 2 to 5 nucleotides in length. In an embodiment, a loop shares homology with, or is derived from, a naturally occurring sequence. In an embodiment, the loop has at least 50% homology with a loop disclosed herein. In an embodiment, the loop comprises SEQ ID NO: 6588.

Some or all of the nucleotides of the domain can have a modification, e.g., modification described in Section XIII herein.

4) The Second Flagpole Extension

In an embodiment, a dgRNA can comprise additional sequence, 3′ to the crRNA flagpole region or, when present, the first flagpole extension, referred to herein as the second flagpole extension. In an embodiment, the second flagpole extension is, 2-10, 2-9, 2-8, 2-7, 2-6, 2-5, or 2-4 nucleotides in length. In an embodiment, the second flagpole extension is 2, 3, 4, 5, 6, 7, 8, 9, or 10 or more nucleotides in length. In an embodiment, the second flagpole extension comprises SEQ ID NO: 6587.

5) The Tracr:

The tracr is the nucleic acid sequence required for nuclease, e.g., Cas9, binding. Without being bound by theory, it is believed that each Cas9 species is associated with a particular tracr sequence. Tracr sequences are utilized in both sgRNA and in dgRNA systems. In an embodiment, the tracr comprises sequence from, or derived from, an S. pyogenes tracr. In some aspects, the tracr has a portion that hybridizes to the flagpole portion of the crRNA, e.g., has sufficient complementarity to the crRNA flagpole region to form a duplexed region under at least some physiological conditions (sometimes referred to herein as the tracr flagpole region or a tracr domain complementary to the crRNA flagpole region). In embodiments, the domain of the tracr that hybridizes with the crRNA flagpole region comprises at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 nucleotides that hybridize with complementary nucleotides of the crRNA flagpole region. In some aspects, the tracr nucleotides that hybridize with complementary nucleotides of the crRNA flagpole region are contiguous. In some aspects, the tracr nucleotides that hybridize with complementary nucleotides of the crRNA flagpole region are discontinuous, e.g., comprises two or more regions of hybridization separated by nucleotides that do not base pair with nucleotides of the crRNA flagpole region. In some aspects, the portion of the tracr that hybridizes to the crRNA flagpole region comprises, from 5′ to 3′: UAGCAAGUUAAAA (SEQ ID NO: 6597). In some aspects, the portion of the tmcr that hybridizes to the crRNA flagpole regioncomprises, from 5′ to 3′: UAGCAAGUUUAAA (SEQ ID NO: 6598). In embodiments, the sequence that hybridizes with the crRNA flagpole region is disposed on the tracr 5′- to the sequence of the tracr that additionally binds a nuclease, e.g., a Cas molecule, e.g., a Cas9 molecule.

The tracr further comprises a domain that additionally binds to a nuclease, e.g., a Cas molecule, e.g., a Cas9 molecule. Without being bound by theory, it is believed that Cas9 from different species bind to different tracr sequences. In some aspects, the tracr comprises sequence that binds to a S. pyogenes Cas9 molecule. In some aspects, the tracr comprises sequence that binds to a Cas9 molecule disclosed herein. In some aspects, the domain that additionally binds a Cas9 molecule comprises, from 5′ to 3′: UAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGC (SEQ ID NO: 6599). In some aspects the domain that additionally binds a Cas9 molecule comprises, from 5′ to 3′: UAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU (SEQ ID NO: 6600).

In some embodiments, the tracr comprises SEQ ID NO: 6589. In some embodiments, the tracr comprises SEQ ID NO: 6590.

Some or all of the nucleotides of the tracr can have a modification, e.g., modification found in Section XIII herein. In embodiments, the gRNA (e.g., the sgRNA or the tracr and/or crRNA of a dgRNA), e.g., any of the gRNA or gRNA components described above, comprises an inverted abasic residue at the 5′ end, the 3′ end or both the 5′ and 3′ end of the gRNA. In embodiments, the gRNA (e.g., the sgRNA or the tracr and/or crRNA of a dgRNA), e.g., any of the gRNA or gRNA components described above, comprises one or more phosphorothioate bonds between residues at the 5′ end of the polynucleotide, for example, a phosphrothioate bond between the first two 5′ residues, between each of the first three 5′ residues, between each of the first four 5′ residues, or between each of the first five 5′ residues. In embodiments, the gRNA or gRNA component may alternatively or additionally comprise one or more phosphorothioate bonds between residues at the 3′ end of the polynucleotide, for example, a phosphrothioate bond between the first two 3′ residues, between each of the first three 3′ residues, between each of the first four 3′ residues, or between each of the first five 3′ residues. In an embodiment, the gRNA (e.g., the sgRNA or the tracr and/or crRNA of a dgRNA), e.g., any of the gRNA or gRNA components described above, comprises a phosphorothioate bond between each of the first four 5′ residues (e.g., comprises, e.g., consists of, three phosphorothioate bonds at the 5′ end(s)), and a phosphorothioate bond between each of the first four 3′ residues (e.g., comprises, e.g., consists of, three phosphorothioate bonds at the 3′ end(s)). In an embodiment, any of the phosphorothioate modifications described above are combined with an inverted abasic residue at the 5′ end, the 3′ end, or both the 5′ and 3′ ends of the polynucleotide. In such embodiments, the inverted abasic nucleotide may be linked to the 5′ and/or 3′ nucleotide by a phosphate bond or a phosphorothioate bond. In embodiments, the gRNA (e.g., the sgRNA or the tracr and/or crRNA of a dgRNA), e.g., any of the gRNA or gRNA components described above, comprises one or more nucleotides that include a 2′ O-methyl modification. In embodiments, each of the first 1, 2, 3, or more of the 5′ residues comprise a 2′ O-methyl modification. In embodiments, each of the first 1, 2, 3, or more of the 3′ residues comprise a 2′ O-methyl modification. In embodiments, the 4^(th)-to-terminal, 3^(rd)-to-terminal, and 2^(nd)-to-terminal 3′ residues comprise a 2′ O-methyl modification. In embodiments, each of the first 1, 2, 3 or more of the 5′ residues comprise a 2′ O-methyl modification, and each of the first 1, 2, 3 or more of the 3′ residues comprise a 2′ O-methyl modification. In an embodiment, each of the first 3 of the 5′ residues comprise a 2′ O-methyl modification, and each of the first 3 of the 3′ residues comprise a 2′ O-methyl modification. In embodiments, each of the first 3 of the 5′ residues comprise a 2′ O-methyl modification, and the 4^(th)-to-terminal, 3^(rd)-to-terminal, and 2^(nd)-to-terminal 3′ residues comprise a 2′ O-methyl modification. In embodiments, any of the 2′ O-methyl modifications, e.g., as described above, may be combined with one or more phosphorothioate modifications, e.g., as described above, and/or one or more inverted abasic modifications, e.g., as described above. In an embodiment, the gRNA (e.g., the sgRNA or the tracr and/or crRNA of a dgRNA), e.g., any of the gRNA or gRNA components described above, comprises, e.g., consists of, a phosphorothioate bond between each of the first four 5′ residues (e.g., comprises, e.g., consists of three phosphorothioate bonds at the 5′ end of the polynucleotide(s)), a phosphorothioate bond between each of the first four 3′ residues (e.g., comprises, e.g., consists of three phosphorothioate bonds at the 5′ end of the polynucleotide(s)), a 2′ O-methyl modification at each of the first three 5′ residues, and a 2′ O-methyl modification at each of the first three 3′ residues. In an embodiment, the gRNA (e.g., the sgRNA or the tracr and/or crRNA of a dgRNA), e.g., any of the gRNA or gRNA components described above, comprises, e.g., consists of, a phosphorothioate bond between each of the first four 5′ residues (e.g., comprises, e.g., consists of three phosphorothioate bonds at the 5′ end of the polynucleotide(s)), a phosphorothioate bond between each of the first four 3′ residues (e.g., comprises, e.g., consists of three phosphorothioate bonds at the 5′ end of the polynucleotide(s)), a 2′ O-methyl modification at each of the first three 5′ residues, and a 2′ O-methyl modification at each of the 4^(th)-to-terminal, 3^(rd)-to-terminal, and 2^(nd)-to-terminal 3′ residues.

In an embodiment, the gRNA (e.g., the sgRNA or the tracr and/or crRNA of a dgRNA), e.g., any of the gRNA or gRNA components described above, comprises, e.g., consists of, a phosphorothioate bond between each of the first four 5′ residues (e.g., comprises, e.g., consists of three phosphorothioate bonds at the 5′ end of the polynucleotide(s)), a phosphorothioate bond between each of the first four 3′ residues (e.g., comprises, e.g., consists of three phosphorothioate bonds at the 5′ end of the polynucleotide(s)), a 2′ O-methyl modification at each of the first three 5′ residues, a 2′ O-methyl modification at each of the first three 3′ residues, and an additional inverted abasic residue at each of the 5′ and 3′ ends.

In an embodiment, the gRNA (e.g., the sgRNA or the tracr and/or crRNA of a dgRNA), e.g., any of the gRNA or gRNA components described above, comprises, e.g., consists of, a phosphorothioate bond between each of the first four 5′ residues (e.g., comprises, e.g., consists of three phosphorothioate bonds at the 5′ end of the polynucleotide(s)), a phosphorothioate bond between each of the first four 3′ residues (e.g., comprises, e.g., consists of three phosphorothioate bonds at the 5′ end of the polynucleotide(s)), a 2′ O-methyl modification at each of the first three 5′ residues, and a 2′ O-methyl modification at each of the 4^(th)-to-terminal, 3^(rd)-to-terminal, and 2^(nd)-to-terminal 3′ residues, and an additional inverted abasic residue at each of the 5′ and 3′ ends.

In an embodiment, the gRNA is a dgRNA and comprises, e.g., consists of:

crRNA: mN*mN*mN*NNNNNNNNNNNNNNNNNGUUUUAGAGCUAU*mG*mC*mU, where m indicates a base with 2′O-Methyl modification, * indicates a phosphorothioate bond, and N's indicate the residues of the targeting domain, e.g., as described herein, (optionally with an inverted abasic residue at the 5′ and/or 3′ terminus); and tracr: AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACC GAGUCGGUGCUUUUUUU (SEQ ID NO: 6660) (optionally with an inverted abasic residue at the 5′ and/or 3′ terminus).

In an embodiment, the gRNA is a dgRNA and comprises, e.g., consists of:

crRNA: mN*mN*mN*NNNNNNNNNNNNNNNNNGUUUUAGAGCUAU*mG*mC*mU, where m indicates a base with 2′O-Methyl modification, * indicates a phosphorothioate bond, and N's indicate the residues of the targeting domain, e.g., as described herein, (optionally with an inverted abasic residue at the 5′ and/or 3′ terminus); and tracr: mA*mA*mC*AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUG GCACCGAGUCGGUGCUUUU*mU*mU*mU (SEQ ID NO: 346), where m indicates a base with 2′O-Methyl modification, * indicates a phosphorothioate bond, and N's indicate the residues of the targeting domain, e.g., as described herein, (optionally with an inverted abasic residue at the 5′ and/or 3′ terminus).

In an embodiment, the gRNA is a dgRNA and comprises, e.g., consists of:

crRNA: mN*mN*mN*NNNNNNNNNNNNNNNNNGUUUUAGAGCUAUGCUGUU*mU*mU*mG, where m indicates a base with 2′O-Methyl modification, * indicates a phosphorothioate bond, and N's indicate the residues of the targeting domain, e.g., as described herein, (optionally with an inverted abasic residue at the 5′ and/or 3′ terminus); and tracr: AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACC GAGUCGGUGCUUUUUUU (SEQ ID NO: 6660) (optionally with an inverted abasic residue at the 5′ and/or 3′ terminus).

In an embodiment, the gRNA is a dgRNA and comprises, e.g., consists of:

crRNA: mN*mN*mN*NNNNNNNNNNNNNNNNNGUUUUAGAGCUAUGCUGUU*mU*mU*mG, where m indicates a base with 2′O-Methyl modification, * indicates a phosphorothioate bond, and N's indicate the residues of the targeting domain, e.g., as described herein, (optionally with an inverted abasic residue at the 5′ and/or 3′ terminus); and tracr: mA*mA*mC*AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUG GCACCGAGUCGGUGCUUUU*mU*mU*mU (SEQ ID NO: 346), where m indicates a base with 2′O-Methyl modification, and * indicates a phosphorothioate bond (optionally with an inverted abasic residue at the 5′ and/or 3′ terminus).

In an embodiment, the gRNA is a dgRNA and comprises, e.g., consists of:

crRNA: NNNNNNNNNNNNNNNNNNNNGUUUUAGAGCUAUGCUGUUUUG, where N's indicate the residues of the targeting domain, e.g., as described herein, (optionally with an inverted abasic residue at the 5′ and/or 3′ terminus); and tracr: mA*mA*mC*AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUG GCACCGAGUCGGUGCUUUU*mU*mU*mU (SEQ ID NO: 346), where m indicates a base with 20-Methyl modification, and * indicates a phosphorothioate bond (optionally with an inverted abasic residue at the 5′ and/or 3′ terminus).

In an embodiment, the gRNA is a sgRNA and comprises, e.g., consists of:

NNNNNNNNNNNNNNNNNNNNGUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUA GUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU, where m indicates a base with 2′O-Methyl modification, * indicates a phosphorothioate bond, and N's indicate the residues of the targeting domain, e.g., as described herein, (optionally with an inverted abasic residue at the 5′ and/or 3′ terminus).

In an embodiment, the gRNA is a sgRNA and comprises, e.g., consists of:

mN*mN*mN*NNNNNNNNNNNNNNNNNGUUUUAGAGCUAGAAAUAGCAAGUUAAAAUA AGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCU*mU*mU*mU, where m indicates a base with 2′O-Methyl modification, * indicates a phosphorothioate bond, and N's indicate the residues of the targeting domain, e.g., as described herein, (optionally with an inverted abasic residue at the 5′ and/or 3′ terminus).

In an embodiment, the gRNA is a sgRNA and comprises, e.g., consists of:

mN*mN*mN*NNNNNNNNNNNNNNNNNGUUUUAGAGCUAGAAAUAGCAAGUUAAAAUA AGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCmU*mU*mU*U, where m indicates a base with 2′O-Methyl modification, * indicates a phosphorothioate bond, and N's indicate the residues of the targeting domain, e.g., as described herein, (optionally with an inverted abasic residue at the 5′ and/or 3′ terminus).

6) First Tracr Extension

Where the gRNA comprises a first flagpole extension, the tracr may comprise a first tracr extension. The first tracr extension may comprise nucleotides that are complementary, e.g., 80%, 85%, 90%, 95% or 99%, e.g., fully complementary, with nucleotides of the first flagpole extension. In some aspects, the first tracr extension nucleotides that hybridize with complementary nucleotides of the first flagpole extension are contiguous. In some aspects, the first tracr extension nucleotides that hybridize with complementary nucleotides of the first flagpole extension are discontinuous, e.g., comprises two or more regions of hybridization separated by nucleotides that do not base pair with nucleotides of the first flagpole extension. In some aspects, the first tracr extension comprises at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more nucleotides. In some aspects, the first tracr extension comprises SEQ ID NO: 6591. In some aspects the first tracr extension comprises nucleic acid that is at least 80%, 85%, 90%, 95% or 99% homology to SEQ ID NO: 6591.

Some or all of the nucleotides of the first tracr extension can have a modification, e.g., modification found in Section XIII herein.

In some embodiments, the sgRNA may comprise, from 5′ to 3′, disposed 3′ to the targeting domain:

a) (SEQ ID NO: 6601) GUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAAC UUGAAAAAGUGGCACCGAGUCGGUGC; b) (SEQ ID NO: 6602) GUUUAAGAGCUAGAAAUAGCAAGUUUAAAUAAGGCUAGUCCGUUAUCAAC UUGAAAAAGUGGCACCGAGUCGGUGC; c) (SEQ ID NO: 6603) GUUUUAGAGCUAUGCUGGAAACAGCAUAGCAAGUUAAAAUAAGGCUAGUC CGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGC; d) (SEQ ID NO: 6604) GUUUAAGAGCUAUGCUGGAAACAGCAUAGCAAGUUUAAAUAAGGCUAGUC CGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGC; e) any of a) to d), above, further comprising, at the 3′ end, at least 1, 2, 3, 4, 5, 6 or 7 uracil (U) nucleotides, e.g., 1, 2, 3, 4, 5, 6, or 7 uracil (U) nucleotides; f) any of a) to d), above, further comprising, at the 3′ end, at least 1, 2, 3, 4, 5, 6 or 7 adenine (A) nucleotides, e.g., 1, 2, 3, 4, 5, 6, or 7 adenine (A) nucleotides; or g) any of a) to f), above, further comprising, at the 5′ end (e.g., at the 5′ terminus, e.g., 5′ to the targeting domain), at least 1, 2, 3, 4, 5, 6 or 7 adenine (A) nucleotides, e.g., 1, 2, 3, 4, 5, 6, or 7 adenine (A) nucleotides. In embodiments, any of a) to g) above is disposed directly 3′ to the targeting domain.

In an embodiment, a sgRNA of the invention comprises, e.g., consists of, from 5′ to 3′: [targeting domain]-

(SEQ ID NO: 7811) GUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAAC UUGAAAAAGUGGCACCGAGUCGGUGCUUUU.

In an embodiment, a sgRNA of the invention comprises, e.g., consists of, from 5′ to 3′: [targeting domain]-

(SEQ ID NO: 7807) GUUUAAGAGCUAUGCUGGAAACAGCAUAGCAAGUUUAAAUAAGGCUAGUC CGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU.

In some embodiments, the dgRNA may comprise:

A crRNA comprising, from 5′ to 3′, preferrably disposed directly 3′ to the targeting domain:

a) (SEQ ID NO: 6584) GUUUUAGAGCUA; b) (SEQ ID NO: 6585) GUUUAAGAGCUA; c) (SEQ ID NO: 6605) GUUUUAGAGCUAUGCUG; d) (SEQ ID NO: 6606) GUUUAAGAGCUAUGCUG; e) (SEQ ID NO: 6607) GUUUUAGAGCUAUGCUGUUUUG; f) (SEQ ID NO: 6608) GUUUAAGAGCUAUGCUGUUUUG; or g) (SEQ ID NO: 7806) GUUUUAGAGCUAUGCU: and a tracr comprising, from 5′ to 3′:

a) (SEQ ID NO: 6589) UAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACC GAGUCGGUGC; b) (SEQ ID NO: 6590) UAGCAAGUUUAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACC GAGUCGGUGC; c) (SEQ ID NO: 6609) CAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUG GCACCGAGUCGGUGC; d) (SEQ ID NO: 6610) CAGCAUAGCAAGUUUAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUG GCACCGAGUCGGUGC; e) (SEQ ID NO: 6660) AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG UGGCACCGAGUCGGUGCUUUUUUU; f) (SEQ ID NO: 6661) AACAGCAUAGCAAGUUUAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG UGGCACCGAGUCGGUGCUUUUUUU; g) (SEQ ID NO: 7812) AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG UGGCACCGAGUCGGUGC h) (SEQ ID NO: 7807) GUUUAAGAGCUAUGCUGGAAACAGCAUAGCAAGUUUAAAUAAGGCUAGUC CGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU; i) (SEQ ID NO: 7808) AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGG CACCGAGUCGGUGCUUU; j) (SEQ ID NO: 7809) GUUGGAACCAUUCAAAACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUU AUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUU; k) any of a) to j), above, further comprising, at the 3′ end, at least 1, 2, 3, 4, 5, 6 or 7 uracil (U) nucleotides, e.g., 1, 2, 3, 4, 5, 6, or 7 uracil (U) nucleotides; l) any of a) to j), above, further comprising, at the 3′ end, at least 1, 2, 3, 4, 5, 6 or 7 adenine (A) nucleotides, e.g., 1, 2, 3, 4, 5, 6, or 7 adenine (A) nucleotides; or m) any of a) to l), above, further comprising, at the 5′ end (e.g., at the 5′ terminus), at least 1, 2, 3, 4, 5, 6 or 7 adenine (A) nucleotides, e.g., 1, 2, 3, 4, 5, 6, or 7 adenine (A) nucleotides.

In an embodiment, the sequence of k), above comprises the 3′ sequence UUUUUU, e.g., if a U6 promoter is used for transcription. In an embodiment, the sequence of k), above, comprises the 3′ sequence UUUU, e.g., if an HI promoter is used for transcription. In an embodiment, sequence of k), above, comprises variable numbers of 3′ U's depending, e.g., on the termination signal of the pol-III promoter used. In an embodiment, the sequence of k), above, comprises variable 3′ sequence derived from the DNA template if a T7 promoter is used. In an embodiment, the sequence of k), above, comprises variable 3′ sequence derived from the DNA template, e.g., if in vitro transcription is used to generate the RNA molecule. In an embodiment, the sequence of k), above, comprises variable 3′ sequence derived from the DNA template, e.g, if a pol-II promoter is used to drive transcription.

In an embodiment, the crRNA comprises, e.g., consists of, a targeting domain and, disposed 3′ to the targeting domain (e.g., disposed directly 3′ to the targeting domain), a sequence comprising, e.g., consisting of, SEQ ID NO: 6607, and the tracr comprises, e.g., consists of

(SEQ ID NO: 6660) AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG UGGCACCGAGUCGGUGCUUUUUUU.

In an embodiment, the crRNA comprises, e.g., consists of, a targeting domain and, disposed 3′ to the targeting domain (e.g., disposed directly 3′ to the targeting domain), a sequence comprising, e.g., consisting of, SEQ ID NO: 6608, and the tracr comprises, e.g., consists of,

(SEQ ID NO: 6661) AACAGCAUAGCAAGUUUAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG UGGCACCGAGUCGGUGCUUUUUUU.

In an embodiment, the crRNA comprises, e.g., consists of, a targeting domain and, disposed 3′ to the targeting domain (e.g., disposed directly 3′ to the targeting domain), a sequence comprising, e.g., consisting of, GUUUUAGAGCUAUGCU (SEQ ID NO: 7806), and the tracr comprises, e.g., consists of,

(SEQ ID NO: 7807) GUUUAAGAGCUAUGCUGGAAACAGCAUAGCAAGUUUAAAUAAGGCUAGUC CGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU.

In an embodiment, the crRNA comprises, e.g., consists of, a targeting domain and, disposed 3′ to the targeting domain (e.g., disposed directly 3′ to the targeting domain), a sequence comprising, e.g., consisting of, GUUUUAGAGCUAUGCU (SEQ ID NO: 7806), and the tracr comprises, e.g., consists of,

(SEQ ID NO: 7808) AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGG CACCGAGUCGGUGCUUU.

In an embodiment, the crRNA comprises, e.g., consists of, a targeting domain and, disposed 3′ to the targeting domain (e.g., disposed directly 3′ to the targeting domain), a sequence comprising, e.g., consisting of, GUUUUAGAGCUAUGCUGUUUUG (SEQ ID NO: 6607), and the tracr comprises, e.g., consists of,

(SEQ ID NO: 7809) GUUGGAACCAUUCAAAACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUU AUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUU.

II. Targeting Domains Useful for Altering Expression of Globin Genes

Provided in the tables below are targeting domains for gRNA molecules for use in the various aspect of the present invention, for example, in altering expression of globin genes, for example, a fetal hemoglobin gene or a hemoglobin beta gene.

TABLE 1 gRNA targeting domains directed to BLC11a exon regions SEQ Target Targeting Site ID Id. Target Region Strand (hg38) gRNA Targeting Domain NO: 53335_5_1 BCL11a Exon 5 + chr2: 60451170-60451195 CAGUCAUUAUUUAUUAUGA 400 AUAAGC 53335_5_2 BCL11a Exon 5 + chr2: 60451196-60451221 GGAAAUAAUUCACAUGCCA 401 AUUAUU 53335_5_3 BCL11a Exon 5 + chr2: 60451217-60451242 UAUUUGGCUAUCUUUUCAC 402 UAAGCU 53335_5_4 BCL11a Exon 5 + chr2: 60451233-60451258 CACUAAGCUAGGUAAUCUA 403 GCCAGA 53335_5_5 BCL11a Exon 5 + chr2: 60451236-60451261 UAAGCUAGGUAAUCUAGCC 404 AGAAGG 53335_5_6 BCL11a Exon 5 + chr2: 60451241-60451266 UAGGUAAUCUAGCCAGAAG 405 GUGGAU 53335_5_7 BCL11a Exon 5 + chr2: 60451245-60451270 UAAUCUAGCCAGAAGGUGG 406 AUAGGU 53335_5_8 BCL11a Exon 5 + chr2: 60451261-60451286 UGGAUAGGUAGGAUUUUCC 407 CCACUU 53335_5_9 BCL11a Exon 5 + chr2: 60451268-60451293 GUAGGAUUUUCCCCACUUA 408 GGUUCA 53335_5_10 BCL11a Exon 5 + chr2: 60451295-60451320 GCCUGUAUGUGAAUCUACA 409 GCACAC 53335_5_11 BCL11a Exon 5 + chr2: 60451359-60451384 UGCUAUGUUGUUUCUAAUU 410 CUCUUC 53335_5_12 BCL11a Exon 5 + chr2: 60451414-60451439 UGAGAAAAGUUCUGUGCAA 411 AUUAAC 53335_5_13 BCL11a Exon 5 + chr2: 60451415-60451440 GAGAAAAGUUCUGUGCAAA 412 UUAACU 53335_5_14 BCL11a Exon 5 + chr2: 60451462-60451487 CCUGUUUGUAGAUGUAACU 413 UAUUUG 53335_5_15 BCL11a Exon 5 + chr2: 60451477-60451502 AACUUAUUUGUGGCACUAA 414 UUUCUA 53335_5_16 BCL11a Exon 5 + chr2: 60451625-60451650 GUCUGCAUUAAGAUAUAUU 415 UCCUGA 53335_5_17 BCL11a Exon 5 + chr2: 60451630-60451655 CAUUAAGAUAUAUUUCCUG 416 AAGGUU 53335_5_18 BCL11a Exon 5 + chr2: 60451631-60451656 AUUAAGAUAUAUUUCCUGA 417 AGGUUU 53335_5_19 BCL11a Exon 5 + chr2: 60451687-60451712 ACUACUGACAUUUAUCACC 418 UUCUUU 53335_5_20 BCL11a Exon 5 + chr2: 60451754-60451779 UUAAAAGACAAAUUCAAAU 419 CCUGCA 53335_5_21 BCL11a Exon 5 + chr2: 60451786-60451811 CACCAAAAGCAUAUAUUUG 420 AAAAAC 53335_5_22 BCL11a Exon 5 + chr2: 60451792-60451817 AAGCAUAUAUUUGAAAAAC 421 AGGAUU 53335_5_23 BCL11a Exon 5 + chr2: 60451819-60451844 GCGUGCCAUAUUAUGCAUU 422 AUUUAA 53335_5_24 BCL11a Exon 5 + chr2: 60451847-60451872 UAUGCAAAUUAUAAGUCAG 423 ACAGUU 53335_5_25 BCL11a Exon 5 + chr2: 60451971-60451996 UUGAAAAUUUAUGCCAUCU 424 GAUAAG 53335_5_26 BCL11a Exon 5 + chr2: 60452037-60452062 AAAUCUGUUCCUCCUACCC 425 ACCCGA 53335_5_27 BCL11a Exon 5 + chr2: 60452038-60452063 AAUCUGUUCCUCCUACCCA 426 CCCGAU 53335_5_28 BCL11a Exon 5 + chr2: 60452048-60452073 UCCUACCCACCCGAUGGGU 427 GUCUGU 53335_5_29 BCL11a Exon 5 + chr2: 60452055-60452080 CACCCGAUGGGUGUCUGUA 428 GGAAAC 53335_5_30 BCL11a Exon 5 + chr2: 60452203-60452228 AGACAACAUAGAAUGUAUA 429 GAAACA 53335_5_31 BCL11a Exon 5 + chr2: 60452204-60452229 GACAACAUAGAAUGUAUAG 430 AAACAA 53335_5_32 BCL11a Exon 5 + chr2: 60452205-60452230 ACAACAUAGAAUGUAUAGA 431 AACAAG 53335_5_33 BCL11a Exon 5 + chr2: 60452209-60452234 CAUAGAAUGUAUAGAAACA 432 AGGGGU 53335_5_34 BCL11a Exon 5 + chr2: 60452210-60452235 AUAGAAUGUAUAGAAACAA 433 GGGGUU 53335_5_35 BCL11a Exon 5 + chr2: 60452211-60452236 UAGAAUGUAUAGAAACAAG 434 GGGUUG 53335_5_36 BCL11a Exon 5 + chr2: 60452237-60452262 GGACUCAUGCGCAUUUCCA 435 CAAUAC 53335_5_37 BCL11a Exon 5 + chr2: 60452245-60452270 GCGCAUUUCCACAAUACAG 436 GUAAUU 53335_5_38 BCL11a Exon 5 + chr2: 60452249-60452274 AUUUCCACAAUACAGGUAA 437 UUAGGU 53335_5_39 BCL11a Exon 5 + chr2: 60452253-60452278 CCACAAUACAGGUAAUUAG 438 GUUGGC 53335_5_40 BCL11a Exon 5 + chr2: 60452263-60452288 GGUAAUUAGGUUGGCUGGU 439 UUCAGA 53335_5_41 BCL11a Exon 5 + chr2: 60452264-60452289 GUAAUUAGGUUGGCUGGUU 440 UCAGAA 53335_5_42 BCL11a Exon 5 + chr2: 60452269-60452294 UAGGUUGGCUGGUUUCAGA 441 AGGGCC 53335_5_43 BCL11a Exon 5 + chr2: 60452270-60452295 AGGUUGGCUGGUUUCAGAA 442 GGGCCA 53335_5_44 BCL11a Exon 5 + chr2: 60452291-60452316 GCCAGGGCAUCACUCAUGA 443 CAGCGA 53335_5_45 BCL11a Exon 5 + chr2: 60452298-60452323 CAUCACUCAUGACAGCGAU 444 GGUCCA 53335_5_46 BCL11a Exon 5 + chr2: 60452299-60452324 AUCACUCAUGACAGCGAUG 445 GUCCAC 53335_5_47 BCL11a Exon 5 + chr2: 60452311-60452336 AGCGAUGGUCCACGGGCCC 446 UCUCUA 53335_5_48 BCL11a Exon 5 + chr2: 60452312-60452337 GCGAUGGUCCACGGGCCCU 447 CUCUAU 53335_5_49 BCL11a Exon 5 + chr2: 60452335-60452360 AUGGGACUGAUUCACUGUU 448 CCAAUG 53335_5_50 BCL11a Exon 5 + chr2: 60452336-60452361 UGGGACUGAUUCACUGUUC 449 CAAUGU 53335_5_51 BCL11a Exon 5 + chr2: 60452383-60452408 UUUUUAUUAAAAAAUAUAA 450 AUAAAA 53335_5_52 BCL11a Exon 5 + chr2: 60452392-60452417 AAAAAUAUAAAUAAAAUGG 451 CGCUGC 53335_5_53 BCL11a Exon 5 + chr2: 60452398-60452423 AUAAAUAAAAUGGCGCUGC 452 AGGCCU 53335_5_54 BCL11a Exon 5 + chr2: 60452402-60452427 AUAAAAUGGCGCUGCAGGC 453 CUAGGC 53335_5_55 BCL11a Exon 5 + chr2: 60452406-60452431 AAUGGCGCUGCAGGCCUAG 454 GCUGGA 53335_5_56 BCL11a Exon 5 + chr2: 60452416-60452441 CAGGCCUAGGCUGGAAGGA 455 CUCUGC 53335_5_57 BCL11a Exon 5 + chr2: 60452436-60452461 UCUGCAGGACUCUGUCUUC 456 GCACAA 53335_5_58 BCL11a Exon 5 + chr2: 60452444-60452469 ACUCUGUCUUCGCACAACG 457 GCUUCU 53335_5_59 BCL11a Exon 5 + chr2: 60452447-60452472 CUGUCUUCGCACAACGGCU 458 UCUUGG 53335_5_60 BCL11a Exon 5 + chr2: 60452478-60452503 CUGUCAGAAAACAUCACAA 459 ACUAGC 53335_5_61 BCL11a Exon 5 + chr2: 60452505-60452530 GAUGACAGACCACGCUGAC 460 GUCGAC 53335_5_62 BCL11a Exon 5 + chr2: 60452506-60452531 AUGACAGACCACGCUGACG 461 UCGACU 53335_5_63 BCL11a Exon 5 + chr2: 60452509-60452534 ACAGACCACGCUGACGUCG 462 ACUGGG 53335_5_64 BCL11a Exon 5 + chr2: 60452531-60452556 GGGCGGCACGCGUCCACCC 463 CACCCC 53335_5_65 BCL11a Exon 5 + chr2: 60452532-60452557 GGCGGCACGCGUCCACCCC 464 ACCCCU 53335_5_66 BCL11a Exon 5 + chr2: 60452533-60452558 GCGGCACGCGUCCACCCCA 465 CCCCUG 53335_5_67 BCL11a Exon 5 + chr2: 60452534-60452559 CGGCACGCGUCCACCCCACC 466 CCUGG 53335_5_68 BCL11a Exon 5 + chr2: 60452559-60452584 GGGCUUCAAAUUUUCUCAG 467 AACUUA 53335_5_69 BCL11a Exon 5 + chr2: 60452560-60452585 GGCUUCAAAUUUUCUCAGA 468 ACUUAA 53335_5_70 BCL11a Exon 5 + chr2: 60452607-60452632 AAACUGCCACACAUCUUGA 469 GCUCUC 53335_5_71 BCL11a Exon 5 + chr2: 60452608-60452633 AACUGCCACACAUCUUGAG 470 CUCUCU 53335_5_72 BCL11a Exon 5 + chr2: 60452623-60452648 UGAGCUCUCUGGGUACUAC 471 GCCGAA 53335_5_73 BCL11a Exon 5 + chr2: 60452624-60452649 GAGCUCUCUGGGUACUACG 472 CCGAAU 53335_5_74 BCL11a Exon 5 + chr2: 60452625-60452650 AGCUCUCUGGGUACUACGC 473 CGAAUG 53335_5_75 BCL11a Exon 5 + chr2: 60452626-60452651 GCUCUCUGGGUACUACGCC 474 GAAUGG 53335_5_76 BCL11a Exon 5 + chr2: 60452649-60452674 GGGGGUGUGUGAAGAACCU 475 AGAAAG 53335_5_77 BCL11a Exon 5 + chr2: 60452653-60452678 GUGUGUGAAGAACCUAGAA 476 AGAGGU 53335_5_78 BCL11a Exon 5 + chr2: 60452662-60452687 GAACCUAGAAAGAGGUUGG 477 AGACAG 53335_5_79 BCL11a Exon 5 − chr2: 60451215-60451240 CUUAGUGAAAAGAUAGCCA 478 AAUAAU 53335_5_80 BCL11a Exon 5 − chr2: 60451256-60451281 GGGAAAAUCCUACCUAUCC 479 ACCUUC 53335_5_81 BCL11a Exon 5 − chr2: 60451281-60451306 CACAUACAGGCCGUGAACC 480 UAAGUG 53335_5_82 BCL11a Exon 5 − chr2: 60451282-60451307 UCACAUACAGGCCGUGAAC 481 CUAAGU 53335_5_83 BCL11a Exon 5 − chr2: 60451283-60451308 UUCACAUACAGGCCGUGAA 482 CCUAAG 53335_5_84 BCL11a Exon 5 − chr2: 60451299-60451324 ACCUGUGUGCUGUAGAUUC 483 ACAUAC 53335_5_85 BCL11a Exon 5 − chr2: 60451350-60451375 UAGAAACAACAUAGCAAAU 484 UAAAAU 53335_5_86 BCL11a Exon 5 − chr2: 60451394-60451419 UCUCAGUUUGGUAUUUUUU 485 ACUGCU 53335_5_87 BCL11a Exon 5 − chr2: 60451411-60451436 AAUUUGCACAGAACUUUUC 486 UCAGUU 53335_5_88 BCL11a Exon 5 − chr2: 60451446-60451471 ACAAACAGGUGGUAAAAAU 487 UCUUUC 53335_5_89 BCL11a Exon 5 − chr2: 60451462-60451487 CAAAUAAGUUACAUCUACA 488 AACAGG 53335_5_90 BCL11a Exon 5 − chr2: 60451465-60451490 CCACAAAUAAGUUACAUCU 489 ACAAAC 53335_5_91 BCL11a Exon 5 − chr2: 60451552-60451577 GAUUUUAGAGGGGGGAAAU 490 UAUAGG 53335_5_92 BCL11a Exon 5 − chr2: 60451555-60451580 GCAGAUUUUAGAGGGGGGA 491 AAUUAU 53335_5_93 BCL11a Exon 5 − chr2: 60451565-60451590 GAAAUUUGGGGCAGAUUUU 492 AGAGGG 53335_5_94 BCL11a Exon 5 − chr2: 60451566-60451591 GGAAAUUUGGGGCAGAUUU 493 UAGAGG 53335_5_95 BCL11a Exon 5 − chr2: 60451567-60451592 AGGAAAUUUGGGGCAGAUU 494 UUAGAG 53335_5_96 BCL11a Exon 5 − chr2: 60451568-60451593 CAGGAAAUUUGGGGCAGAU 495 UUUAGA 53335_5_97 BCL11a Exon 5 − chr2: 60451569-60451594 UCAGGAAAUUUGGGGCAGA 496 UUUUAG 53335_5_98 BCL11a Exon 5 − chr2: 60451582-60451607 UUUAGUACUUACAUCAGGA 497 AAUUUG 53335_5_99 BCL11a Exon 5 − chr2: 60451583-60451608 CUUUAGUACUUACAUCAGG 498 AAAUUU 53335_5_100 BCL11a Exon 5 − chr2: 60451584-60451609 UCUUUAGUACUUACAUCAG 499 GAAAUU 53335_5_101 BCL11a Exon 5 − chr2: 60451592-60451617 AUAAAACUUCUUUAGUACU 500 UACAUC 53335_5_102 BCL11a Exon 5 − chr2: 60451648-60451673 UCUAAUUUUAGGUUCCCAA 501 ACCUUC 53335_5_103 BCL11a Exon 5 − chr2: 60451664-60451689 GUUUCUUAUUAAAUAUUCU 502 AAUUUU 53335_5_104 BCL11a Exon 5 − chr2: 60451707-60451732 CUGGGCGAGCGGUAAAUCC 503 UAAAGA 53335_5_105 BCL11a Exon 5 − chr2: 60451723-60451748 UUAGGAAAGAACAUCACUG 504 GGCGAG 53335_5_106 BCL11a Exon 5 − chr2: 60451730-60451755 AUUUAGCUUAGGAAAGAAC 505 AUCACU 53335_5_107 BCL11a Exon 5 − chr2: 60451731-60451756 AAUUUAGCUUAGGAAAGAA 506 CAUCAC 53335_5_108 BCL11a Exon 5 − chr2: 60451746-60451771 UUGAAUUUGUCUUUUAAUU 507 UAGCUU 53335_5_109 BCL11a Exon 5 − chr2: 60451776-60451801 UAUAUGCUUUUGGUGGCUA 508 CCAUGC 53335_5_110 BCL11a Exon 5 − chr2: 60451788-60451813 CUGUUUUUCAAAUAUAUGC 509 UUUUGG 53335_5_111 BCL11a Exon 5 − chr2: 60451791-60451816 AUCCUGUUUUUCAAAUAUA 510 UGCUUU 53335_5_112 BCL11a Exon 5 − chr2: 60451827-60451852 GCAUACCAUUAAAUAAUGC 511 AUAAUA 53335_5_113 BCL11a Exon 5 − chr2: 60451882-60451907 AUUGCUGUUUAUUAAUGCU 512 GAAGUG 53335_5_114 BCL11a Exon 5 − chr2: 60451949-60451974 CAAGGAGAAUCAAAAUGCA 513 AAACUU 53335_5_115 BCL11a Exon 5 − chr2: 60451950-60451975 UCAAGGAGAAUCAAAAUGC 514 AAAACU 53335_5_116 BCL11a Exon 5 − chr2: 60451972-60451997 GCUUAUCAGAUGGCAUAAA 515 UUUUCA 53335_5_117 BCL11a Exon 5 − chr2: 60451987-60452012 GGGAACUAGGUUACCGCUU 516 AUCAGA 53335_5_118 BCL11a Exon 5 − chr2: 60452005-60452030 GGGCAGGAGAUGUAGGAGG 517 GGAACU 53335_5_119 BCL11a Exon 5 − chr2: 60452012-60452037 GAGAAAUGGGCAGGAGAUG 518 UAGGAG 53335_5_120 BCL11a Exon 5 − chr2: 60452013-60452038 UGAGAAAUGGGCAGGAGAU 519 GUAGGA 53335_5_121 BCL11a Exon 5 − chr2: 60452014-60452039 UUGAGAAAUGGGCAGGAGA 520 UGUAGG 53335_5_122 BCL11a Exon 5 − chr2: 60452017-60452042 GAUUUGAGAAAUGGGCAGG 521 AGAUGU 53335_5_123 BCL11a Exon 5 − chr2: 60452026-60452051 GGAGGAACAGAUUUGAGAA 522 AUGGGC 53335_5_124 BCL11a Exon 5 − chr2: 60452030-60452055 GGUAGGAGGAACAGAUUUG 523 AGAAAU 53335_5_125 BCL11a Exon 5 − chr2: 60452031-60452056 GGGUAGGAGGAACAGAUUU 524 GAGAAA 53335_5_126 BCL11a Exon 5 − chr2: 60452049-60452074 UACAGACACCCAUCGGGUG 525 GGUAGG 53335_5_127 BCL11a Exon 5 − chr2: 60452052-60452077 UCCUACAGACACCCAUCGG 526 GUGGGU 53335_5_128 BCL11a Exon 5 − chr2: 60452056-60452081 UGUUUCCUACAGACACCCA 527 UCGGGU 53335_5_129 BCL11a Exon 5 − chr2: 60452057-60452082 CUGUUUCCUACAGACACCC 528 AUCGGG 53335_5_130 BCL11a Exon 5 − chr2: 60452060-60452085 UACCUGUUUCCUACAGACA 529 CCCAUC 53335_5_131 BCL11a Exon 5 − chr2: 60452061-60452086 GUACCUGUUUCCUACAGAC 530 ACCCAU 53335_5_132 BCL11a Exon 5 − chr2: 60452111-60452136 AAUUUUUAAUGCUUAUAAG 531 ACAAUG 53335_5_133 BCL11a Exon 5 − chr2: 60452155-60452180 ACACAAUAAAUGUUGGAGC 532 UUUAGG 53335_5_134 BCL11a Exon 5 − chr2: 60452158-60452183 UUGACACAAUAAAUGUUGG 533 AGCUUU 53335_5_135 BCL11a Exon 5 − chr2: 60452167-60452192 UGCUUAACAUUGACACAAU 534 AAAUGU 53335_5_136 BCL11a Exon 5 − chr2: 60452256-60452281 CCAGCCAACCUAAUUACCU 535 GUAUUG 53335_5_137 BCL11a Exon 5 − chr2: 60452295-60452320 ACCAUCGCUGUCAUGAGUG 536 AUGCCC 53335_5_138 BCL11a Exon 5 − chr2: 60452323-60452348 GAAUCAGUCCCAUAGAGAG 537 GGCCCG 53335_5_139 BCL11a Exon 5 − chr2: 60452330-60452355 GAACAGUGAAUCAGUCCCA 538 UAGAGA 53335_5_140 BCL11a Exon 5 − chr2: 60452331-60452356 GGAACAGUGAAUCAGUCCC 539 AUAGAG 53335_5_141 BCL11a Exon 5 − chr2: 60452357-60452382 UAAAAACAAAAAAACAGAC 540 CCACAU 53335_5_142 BCL11a Exon 5 − chr2: 60452423-60452448 GAGUCCUGCAGAGUCCUUC 541 CAGCCU 53335_5_143 BCL11a Exon 5 − chr2: 60452517-60452542 GCGUGCCGCCCAGUCGACG 542 UCAGCG 53335_5_144 BCL11a Exon 5 − chr2: 60452547-60452572 AAAUUUGAAGCCCCCAGGG 543 GUGGGG 53335_5_145 BCL11a Exon 5 − chr2: 60452550-60452575 AGAAAAUUUGAAGCCCCCA 544 GGGGUG 53335_5_146 BCL11a Exon 5 − chr2: 60452551-60452576 GAGAAAAUUUGAAGCCCCC 545 AGGGGU 53335_5_147 BCL11a Exon 5 − chr2: 60452552-60452577 UGAGAAAAUUUGAAGCCCC 546 CAGGGG 53335_5_148 BCL11a Exon 5 − chr2: 60452555-60452580 UUCUGAGAAAAUUUGAAGC 547 CCCCAG 53335_5_149 BCL11a Exon 5 − chr2: 60452556-60452581 GUUCUGAGAAAAUUUGAAG 548 CCCCCA 53335_5_150 BCL11a Exon 5 − chr2: 60452557-60452582 AGUUCUGAGAAAAUUUGAA 549 GCCCCC 53335_5_151 BCL11a Exon 5 − chr2: 60452602-60452627 CUCAAGAUGUGUGGCAGUU 550 UUCGGA 53335_5_152 BCL11a Exon 5 − chr2: 60452606-60452631 AGAGCUCAAGAUGUGUGGC 551 AGUUUU 53335_5_153 BCL11a Exon 5 − chr2: 60452616-60452641 UAGUACCCAGAGAGCUCAA 552 GAUGUG 53335_5_154 BCL11a Exon 5 − chr2: 60452646-60452671 UCUAGGUUCUUCACACACC 553 CCCAUU 53335_4_1 BCL11a Exon 4 + chr2: 60457199-60457224 UUAAUUUUUUUUAUUUUUU 554 CAAUAA 53335_4_2 BCL11a Exon 4 + chr2: 60457200-60457225 UAAUUUUUUUUAUUUUUUC 555 AAUAAA 53335_4_3 BCL11a Exon 4 + chr2: 60457209-60457234 UUAUUUUUUCAAUAAAGGG 556 ACAAAA 53335_4_4 BCL11a Exon 4 + chr2: 60457210-60457235 UAUUUUUUCAAUAAAGGGA 557 CAAAAU 53335_4_5 BCL11a Exon 4 + chr2: 60457222-60457247 AAAGGGACAAAAUGGGUGU 558 AUGAAC 53335_4_6 BCL11a Exon 4 + chr2: 60457259-60457284 ACAACUGCCAAAAAAACAC 559 AGACAG 53335_4_7 BCL11a Exon 4 + chr2: 60457312-60457337 CCAGAAACAAAUACAAUAA 560 AAAGCC 53335_4_8 BCL11a Exon 4 + chr2: 60457328-60457353 UAAAAAGCCAGGUUGUAAU 561 GACCUU 53335_4_9 BCL11a Exon 4 + chr2: 60457401-60457426 CAAAUUAAGUGCCUCUGUU 562 UUGAAC 53335_4_10 BCL11a Exon 4 + chr2: 60457402-60457427 AAAUUAAGUGCCUCUGUUU 563 UGAACA 53335_4_11 BCL11a Exon 4 + chr2: 60457480-60457505 AGUUACGACAAACAGCUUU 564 CAUUAC 53335_4_12 BCL11a Exon 4 + chr2: 60457491-60457516 ACAGCUUUCAUUACAGGAA 565 UAGAAA 53335_4_13 BCL11a Exon 4 + chr2: 60457545-60457570 AUUUACAAAAAAGUAUUGA 566 CUAAAG 53335_4_14 BCL11a Exon 4 + chr2: 60457546-60457571 UUUACAAAAAAGUAUUGAC 567 UAAAGC 53335_4_15 BCL11a Exon 4 + chr2: 60457616-60457641 UAAAUAUAAAGCACCAUUU 568 AGUUUU 53335_4_16 BCL11a Exon 4 + chr2: 60457642-60457667 GGCAAUGAAAAAAACUGCA 569 AAACAU 53335_4_17 BCL11a Exon 4 + chr2: 60457695-60457720 UCUUUCUUUCUUUUACUGC 570 AUAUGA 53335_4_18 BCL11a Exon 4 + chr2: 60457706-60457731 UUUACUGCAUAUGAAGGUA 571 AGAUGC 53335_4_19 BCL11a Exon 4 + chr2: 60457714-60457739 AUAUGAAGGUAAGAUGCUG 572 GAAUGU 53335_4_20 BCL11a Exon 4 + chr2: 60457715-60457740 UAUGAAGGUAAGAUGCUGG 573 AAUGUA 53335_4_21 BCL11a Exon 4 + chr2: 60457725-60457750 AGAUGCUGGAAUGUAGGGU 574 GAUAGA 53335_4_22 BCL11a Exon 4 + chr2: 60457730-60457755 CUGGAAUGUAGGGUGAUAG 575 AAGGAA 53335_4_23 BCL11a Exon 4 + chr2: 60457731-60457756 UGGAAUGUAGGGUGAUAGA 576 AGGAAA 53335_4_24 BCL11a Exon 4 + chr2: 60457792-60457817 UUAGCUUGCAGUACUGCAU 577 ACAGUA 53335_4_25 BCL11a Exon 4 + chr2: 60457799-60457824 GCAGUACUGCAUACAGUAU 578 GGCAGC 53335_4_26 BCL11a Exon 4 + chr2: 60457806-60457831 UGCAUACAGUAUGGCAGCA 579 GGAAAA 53335_4_27 BCL11a Exon 4 + chr2: 60457817-60457842 UGGCAGCAGGAAAAAGGAA 580 CAAAAA 53335_4_28 BCL11a Exon 4 + chr2: 60457863-60457888 ACAGCCAUCCAUGUGACAU 581 UCUAGC 53335_4_29 BCL11a Exon 4 + chr2: 60457887-60457912 CAGGCUCCCCCAAACCGCC 582 AUUAUA 53335_4_30 BCL11a Exon 4 + chr2: 60457996-60458021 CCUGCCAAAUUAAAAAAAU 583 AUACUG 53335_4_31 BCL11a Exon 4 + chr2: 60458031-60458056 UCUUUUUUUUUUCCACUAC 584 CAAAAA 53335_4_32 BCL11a Exon 4 + chr2: 60458178-60458203 AAAGACCAUAAAUGUAUUU 585 UAGCAU 53335_4_33 BCL11a Exon 4 + chr2: 60458274-60458299 UUUUUUUUUUUUACAACCU 586 GAAGAG 53335_4_34 BCL11a Exon 4 + chr2: 60458287-60458312 CAACCUGAAGAGCGGUGUG 587 UAUCCA 53335_4_35 BCL11a Exon 4 + chr2: 60458317-60458342 UAGAAUUUCCACUACCAUU 588 UUUAAA 53335_4_36 BCL11a Exon 4 + chr2: 60458350-60458375 AAGUCUUGUAACACCACCA 589 AGACAA 53335_4_37 BCL11a Exon 4 + chr2: 60458564-60458589 UAAGUAAGCUCAAUAGUCA 590 AGUAAA 53335_4_38 BCL11a Exon 4 + chr2: 60458568-60458593 UAAGCUCAAUAGUCAAGUA 591 AAUGGC 53335_4_39 BCL11a Exon 4 + chr2: 60458677-60458702 UUCCCUUAAGUAUAGACCU 592 GUAAAC 53335_4_40 BCL11a Exon 4 + chr2: 60458678-60458703 UCCCUUAAGUAUAGACCUG 593 UAAACU 53335_4_41 BCL11a Exon 4 + chr2: 60458717-60458742 GUGCACUUAAUUGUCCUAU 594 CUGAGC 53335_4_42 BCL11a Exon 4 + chr2: 60458775-60458800 AUUAGAGAAAAGAUACAGA 595 UAUCAC 53335_4_43 BCL11a Exon 4 + chr2: 60458806-60458831 AGUCAAGUGCUAUUUGAAC 596 ACCAAC 53335_4_44 BCL11a Exon 4 + chr2: 60458807-60458832 GUCAAGUGCUAUUUGAACA 597 CCAACU 53335_4_45 BCL11a Exon 4 + chr2: 60458808-60458833 UCAAGUGCUAUUUGAACAC 598 CAACUG 53335_4_46 BCL11a Exon 4 + chr2: 60458904-60458929 GUUAACACAAAUAGCACAC 599 AGUGUA 53335_4_47 BCL11a Exon 4 + chr2: 60458930-60458955 GGAAAAGAAAUGAAGUACA 600 ACUUUU 53335_4_48 BCL11a Exon 4 + chr2: 60458931-60458956 GAAAAGAAAUGAAGUACAA 601 CUUUUA 53335_4_49 BCL11a Exon 4 + chr2: 60459074-60459099 CUUAUAUACCUGUUCUAGU 602 UUUAAA 53335_4_50 BCL11a Exon 4 + chr2: 60459165-60459190 UAUUGUCAGCCUCUUCCUU 603 UCAAUA 53335_4_51 BCL11a Exon 4 + chr2: 60459174-60459199 CCUCUUCCUUUCAAUAUGG 604 UAUACA 53335_4_52 BCL11a Exon 4 + chr2: 60459223-60459248 UGUCCACUUGACAACCAAG 605 UAGAUC 53335_4_53 BCL11a Exon 4 + chr2: 60459238-60459263 CAAGUAGAUCUGGAUCUAU 606 UUCUUU 53335_4_54 BCL11a Exon 4 + chr2: 60459322-60459347 UUACUAGUGUAUUUAAUUG 607 CGUUCC 53335_4_55 BCL11a Exon 4 + chr2: 60459323-60459348 UACUAGUGUAUUUAAUUGC 608 GUUCCA 53335_4_56 BCL11a Exon 4 + chr2: 60459378-60459403 UCAUUGUUUAAAAAAAAUA 609 AAACUU 53335_4_57 BCL11a Exon 4 + chr2: 60459379-60459404 CAUUGUUUAAAAAAAAUAA 610 AACUUU 53335_4_58 BCL11a Exon 4 + chr2: 60459413-60459438 AGCCCAUUUCUUUUAAGCU 611 CUCACC 53335_4_59 BCL11a Exon 4 + chr2: 60459435-60459460 ACCAGGAGCAAAGUAGCUU 612 UUAUAC 53335_4_60 BCL11a Exon 4 + chr2: 60459470-60459495 AGUUUUGUUUAUAAAAUUA 613 AACUAA 53335_4_61 BCL11a Exon 4 + chr2: 60459490-60459515 ACUAAAGGAAAAAUGAUGA 614 UUAACU 53335_4_62 BCL11a Exon 4 + chr2: 60459499-60459524 AAAAUGAUGAUUAACUAGG 615 ACAUAA 53335_4_63 BCL11a Exon 4 + chr2: 60459500-60459525 AAAUGAUGAUUAACUAGGA 616 CAUAAU 53335_4_64 BCL11a Exon 4 + chr2: 60459513-60459538 CUAGGACAUAAUGGGUCAU 617 CUUUUU 53335_4_65 BCL11a Exon 4 + chr2: 60459564-60459589 AUAUAGAAUUAUAUGCUAG 618 UUCCUA 53335_4_66 BCL11a Exon 4 + chr2: 60459632-60459657 UAACAAGUAGAAAGAACCA 619 UCGAUG 53335_4_67 BCL11a Exon 4 + chr2: 60459649-60459674 CAUCGAUGUGGUUUUAAUA 620 GAUCCA 53335_4_68 BCL11a Exon 4 + chr2: 60459718-60459743 GUUUUUCUGUUAAUUUGUC 621 AAUUCA 53335_4_69 BCL11a Exon 4 + chr2: 60459818-60459843 UCAGUGCUAUCUAUUCUGU 622 CUAUAG 53335_4_70 BCL11a Exon 4 + chr2: 60459819-60459844 CAGUGCUAUCUAUUCUGUC 623 UAUAGA 53335_4_71 BCL11a Exon 4 + chr2: 60459900-60459925 UAUGUAUUACAGAAUGUAU 624 GCAGCA 53335_4_72 BCL11a Exon 4 + chr2: 60459937-60459962 CUCUCUCUCUCUUUUUCUC 625 UCAGAA 53335_4_73 BCL11a Exon 4 + chr2: 60459943-60459968 CUCUCUUUUUCUCUCAGAA 626 CGGAAC 53335_4_74 BCL11a Exon 4 + chr2: 60459977-60460002 CAACAUGUUUGCUCAGCAA 627 CGAAUU 53335_4_75 BCL11a Exon 4 + chr2: 60459978-60460003 AACAUGUUUGCUCAGCAAC 628 GAAUUA 53335_4_76 BCL11a Exon 4 + chr2: 60460068-60460093 ACAUGUAAAUUAUUGCACA 629 AGAGAA 53335_4_77 BCL11a Exon 4 + chr2: 60460126-60460151 GCCCCAUACAGAUCAUGCA 630 UUCAAA 53335_4_78 BCL11a Exon 4 + chr2: 60460140-60460165 AUGCAUUCAAACGGUGAGA 631 ACAUAA 53335_4_79 BCL11a Exon 4 + chr2: 60460193-60460218 AAAGAAAAAGAAAAAGAAA 632 AAAAAC 53335_4_80 BCL11a Exon 4 + chr2: 60460201-60460226 AGAAAAAGAAAAAAAACAG 633 GUGUGC 53335_4_81 BCL11a Exon 4 + chr2: 60460269-60460294 UGUUUGUUUGUUUGUUUAA 634 AUCACA 53335_4_82 BCL11a Exon 4 + chr2: 60460270-60460295 GUUUGUUUGUUUGUUUAAA 635 UCACAU 53335_4_83 BCL11a Exon 4 + chr2: 60460291-60460316 ACAUGGGACUAGAAAAAAA 636 UCCUAC 53335_4_84 BCL11a Exon 4 + chr2: 60460292-60460317 CAUGGGACUAGAAAAAAAU 637 CCUACA 53335_4_85 BCL11a Exon 4 + chr2: 60460297-60460322 GACUAGAAAAAAAUCCUAC 638 AGGGAG 53335_4_86 BCL11a Exon 4 + chr2: 60460298-60460323 ACUAGAAAAAAAUCCUACA 639 GGGAGU 53335_4_87 BCL11a Exon 4 + chr2: 60460299-60460324 CUAGAAAAAAAUCCUACAG 640 GGAGUG 53335_4_88 BCL11a Exon 4 + chr2: 60460303-60460328 AAAAAAAUCCUACAGGGAG 641 UGGGGC 53335_4_89 BCL11a Exon 4 + chr2: 60460306-60460331 AAAAUCCUACAGGGAGUGG 642 GGCUGG 53335_4_90 BCL11a Exon 4 + chr2: 60460307-60460332 AAAUCCUACAGGGAGUGGG 643 GCUGGA 53335_4_91 BCL11a Exon 4 + chr2: 60460313-60460338 UACAGGGAGUGGGGCUGGA 644 GGGCGA 53335_4_92 BCL11a Exon 4 + chr2: 60460314-60460339 ACAGGGAGUGGGGCUGGAG 645 GGCGAU 53335_4_93 BCL11a Exon 4 + chr2: 60460315-60460340 CAGGGAGUGGGGCUGGAGG 646 GCGAUG 53335_4_94 BCL11a Exon 4 + chr2: 60460319-60460344 GAGUGGGGCUGGAGGGCGA 647 UGGGGA 53335_4_95 BCL11a Exon 4 + chr2: 60460320-60460345 AGUGGGGCUGGAGGGCGAU 648 GGGGAA 53335_4_96 BCL11a Exon 4 + chr2: 60460321-60460346 GUGGGGCUGGAGGGCGAUG 649 GGGAAG 53335_4_97 BCL11a Exon 4 + chr2: 60460326-60460351 GCUGGAGGGCGAUGGGGAA 650 GGGGAG 53335_4_98 BCL11a Exon 4 + chr2: 60460335-60460360 CGAUGGGGAAGGGGAGUGG 651 UGAAAA 53335_4_99 BCL11a Exon 4 + chr2: 60460336-60460361 GAUGGGGAAGGGGAGUGGU 652 GAAAAA 53335_4_100 BCL11a Exon 4 + chr2: 60460337-60460362 AUGGGGAAGGGGAGUGGUG 653 AAAAAG 53335_4_101 BCL11a Exon 4 + chr2: 60460338-60460363 UGGGGAAGGGGAGUGGUGA 654 AAAAGG 53335_4_102 BCL11a Exon 4 + chr2: 60460345-60460370 GGGGAGUGGUGAAAAAGGG 655 GGUGUC 53335_4_103 BCL11a Exon 4 + chr2: 60460348-60460373 GAGUGGUGAAAAAGGGGGU 656 GUCAGG 53335_4_104 BCL11a Exon 4 + chr2: 60460349-60460374 AGUGGUGAAAAAGGGGGUG 657 UCAGGU 53335_4_105 BCL11a Exon 4 + chr2: 60460356-60460381 AAAAAGGGGGUGUCAGGUG 658 GGAGUG 53335_4_106 BCL11a Exon 4 + chr2: 60460357-60460382 AAAAGGGGGUGUCAGGUGG 659 GAGUGA 53335_4_107 BCL11a Exon 4 + chr2: 60460360-60460385 AGGGGGUGUCAGGUGGGAG 660 UGAGGG 53335_4_108 BCL11a Exon 4 + chr2: 60460361-60460386 GGGGGUGUCAGGUGGGAGU 661 GAGGGA 53335_4_109 BCL11a Exon 4 + chr2: 60460362-60460387 GGGGUGUCAGGUGGGAGUG 662 AGGGAG 53335_4_110 BCL11a Exon 4 + chr2: 60460442-60460467 GUGCCAUUUUUUCAUGUGU 663 UUCUCC 53335_4_111 BCL11a Exon 4 + chr2: 60460443-60460468 UGCCAUUUUUUCAUGUGUU 664 UCUCCA 53335_4_112 BCL11a Exon 4 + chr2: 60460462-60460487 UCUCCAGGGUACUGUACAC 665 GCUAAA 53335_4_113 BCL11a Exon 4 + chr2: 60460505-60460530 ACAUUUGUAAACGUCCUUC 666 CCCACC 53335_4_114 BCL11a Exon 4 + chr2: 60460527-60460552 ACCUGGCCAUGCGUUUUCA 667 UGUGCC 53335_4_115 BCL11a Exon 4 + chr2: 60460544-60460569 CAUGUGCCUGGUGAGCUUG 668 CUACUC 53335_4_116 BCL11a Exon 4 + chr2: 60460545-60460570 AUGUGCCUGGUGAGCUUGC 669 UACUCU 53335_4_117 BCL11a Exon 4 + chr2: 60460551-60460576 CUGGUGAGCUUGCUACUCU 670 GGGCAC 53335_4_118 BCL11a Exon 4 + chr2: 60460579-60460604 CAUAGUUGCACAGCUCGCA 671 UUUAUA 53335_4_119 BCL11a Exon 4 + chr2: 60460595-60460620 GCAUUUAUAAGGCCUUUCG 672 CCCGUG 53335_4_120 BCL11a Exon 4 + chr2: 60460607-60460632 CCUUUCGCCCGUGUGGCUU 673 CUCCUG 53335_4_121 BCL11a Exon 4 + chr2: 60460686-60460711 UCGCUGCGUCUGCCCUCUU 674 UUGAGC 53335_4_122 BCL11a Exon 4 + chr2: 60460687-60460712 CGCUGCGUCUGCCCUCUUU 675 UGAGCU 53335_4_123 BCL11a Exon 4 + chr2: 60460696-60460721 UGCCCUCUUUUGAGCUGGG 676 CCUGCC 53335_4_124 BCL11a Exon 4 + chr2: 60460697-60460722 GCCCUCUUUUGAGCUGGGC 677 CUGCCC 53335_4_125 BCL11a Exon 4 + chr2: 60460702-60460727 CUUUUGAGCUGGGCCUGCC 678 CGGGCC 53335_4_126 BCL11a Exon 4 + chr2: 60460715-60460740 CCUGCCCGGGCCCGGACCA 679 CUAAUA 53335_4_127 BCL11a Exon 4 + chr2: 60460716-60460741 CUGCCCGGGCCCGGACCAC 680 UAAUAU 53335_4_128 BCL11a Exon 4 + chr2: 60460717-60460742 UGCCCGGGCCCGGACCACU 681 AAUAUG 53335_4_129 BCL11a Exon 4 + chr2: 60460776-60460801 CCCGAGAUCCCUCCGUCCA 682 GCUCCC 53335_4_130 BCL11a Exon 4 + chr2: 60460777-60460802 CCGAGAUCCCUCCGUCCAG 683 CUCCCC 53335_4_131 BCL11a Exon 4 + chr2: 60460780-60460805 AGAUCCCUCCGUCCAGCUC 684 CCCGGG 53335_4_132 BCL11a Exon 4 + chr2: 60460785-60460810 CCUCCGUCCAGCUCCCCGG 685 GCGGUG 53335_4_133 BCL11a Exon 4 + chr2: 60460812-60460837 GAGAAGCGCAAACUCCCGU 686 UCUCCG 53335_4_134 BCL11a Exon 4 + chr2: 60460827-60460852 CCGUUCUCCGAGGAGUGCU 687 CCGACG 53335_4_135 BCL11a Exon 4 + chr2: 60460830-60460855 UUCUCCGAGGAGUGCUCCG 688 ACGAGG 53335_4_136 BCL11a Exon 4 + chr2: 60460837-60460862 AGGAGUGCUCCGACGAGGA 689 GGCAAA 53335_4_137 BCL11a Exon 4 + chr2: 60460848-60460873 GACGAGGAGGCAAAAGGCG 690 AUUGUC 53335_4_138 BCL11a Exon 4 + chr2: 60460865-60460890 CGAUUGUCUGGAGUCUCCG 691 AAGCUA 53335_4_139 BCL11a Exon 4 + chr2: 60460869-60460894 UGUCUGGAGUCUCCGAAGC 692 UAAGGA 53335_4_140 BCL11a Exon 4 + chr2: 60460870-60460895 GUCUGGAGUCUCCGAAGCU 693 AAGGAA 53335_4_141 BCL11a Exon 4 + chr2: 60460887-60460912 CUAAGGAAGGGAUCUUUGA 694 GCUGCC 53335_4_142 BCL11a Exon 4 + chr2: 60460890-60460915 AGGAAGGGAUCUUUGAGCU 695 GCCUGG 53335_4_143 BCL11a Exon 4 + chr2: 60460902-60460927 UUGAGCUGCCUGGAGGCCG 696 CGUAGC 53335_4_144 BCL11a Exon 4 + chr2: 60460935-60460960 CACUGCGAGUACACGUUCU 697 CCGUGU 53335_4_145 BCL11a Exon 4 + chr2: 60460936-60460961 ACUGCGAGUACACGUUCUC 698 CGUGUU 53335_4_146 BCL11a Exon 4 + chr2: 60460944-60460969 UACACGUUCUCCGUGUUGG 699 GCAUCG 53335_4_147 BCL11a Exon 4 + chr2: 60460948-60460973 CGUUCUCCGUGUUGGGCAU 700 CGCGGC 53335_4_148 BCL11a Exon 4 + chr2: 60460949-60460974 GUUCUCCGUGUUGGGCAUC 701 GCGGCC 53335_4_149 BCL11a Exon 4 + chr2: 60460950-60460975 UUCUCCGUGUUGGGCAUCG 702 CGGCCG 53335_4_150 BCL11a Exon 4 + chr2: 60460951-60460976 UCUCCGUGUUGGGCAUCGC 703 GGCCGG 53335_4_151 BCL11a Exon 4 + chr2: 60460955-60460980 CGUGUUGGGCAUCGCGGCC 704 GGGGGC 53335_4_152 BCL11a Exon 4 + chr2: 60460992-60461017 UUCUCGAGCUUGAUGCGCU 705 UAGAGA 53335_4_153 BCL11a Exon 4 + chr2: 60460993-60461018 UCUCGAGCUUGAUGCGCUU 706 AGAGAA 53335_4_154 BCL11a Exon 4 + chr2: 60460994-60461019 CUCGAGCUUGAUGCGCUUA 707 GAGAAG 53335_4_155 BCL11a Exon 4 + chr2: 60461007-60461032 CGCUUAGAGAAGGGGCUCA 708 GCGAGC 53335_4_156 BCL11a Exon 4 + chr2: 60461008-60461033 GCUUAGAGAAGGGGCUCAG 709 CGAGCU 53335_4_157 BCL11a Exon 4 + chr2: 60461009-60461034 CUUAGAGAAGGGGCUCAGC 710 GAGCUG 53335_4_158 BCL11a Exon 4 + chr2: 60461031-60461056 CUGGGGCUGCCCAGCAGCA 711 GCUUUU 53335_4_159 BCL11a Exon 4 + chr2: 60461036-60461061 GCUGCCCAGCAGCAGCUUU 712 UUGGAC 53335_4_160 BCL11a Exon 4 + chr2: 60461046-60461071 AGCAGCUUUUUGGACAGGC 713 CCCCCG 53335_4_161 BCL11a Exon 4 + chr2: 60461059-60461084 ACAGGCCCCCCGAGGCCGA 714 CUCGCC 53335_4_162 BCL11a Exon 4 + chr2: 60461060-60461085 CAGGCCCCCCGAGGCCGAC 715 UCGCCC 53335_4_163 BCL11a Exon 4 + chr2: 60461061-60461086 AGGCCCCCCGAGGCCGACU 716 CGCCCG 53335_4_164 BCL11a Exon 4 + chr2: 60461072-60461097 GGCCGACUCGCCCGGGGAG 717 CAGCCG 53335_4_165 BCL11a Exon 4 + chr2: 60461099-60461124 GCCAUUAACAGUGCCAUCG 718 UCUAUG 53335_4_166 BCL11a Exon 4 + chr2: 60461112-60461137 CCAUCGUCUAUGCGGUCCG 719 ACUCGC 53335_4_167 BCL11a Exon 4 + chr2: 60461144-60461169 CGAGUCUUCGUCGCAAGUG 720 UCCCUG 53335_4_168 BCL11a Exon 4 + chr2: 60461151-60461176 UCGUCGCAAGUGUCCCUGU 721 GGCCCU 53335_4_169 BCL11a Exon 4 + chr2: 60461157-60461182 CAAGUGUCCCUGUGGCCCU 722 CGGCCU 53335_4_170 BCL11a Exon 4 + chr2: 60461162-60461187 GUCCCUGUGGCCCUCGGCC 723 UCGGCC 53335_4_171 BCL11a Exon 4 + chr2: 60461165-60461190 CCUGUGGCCCUCGGCCUCG 724 GCCAGG 53335_4_172 BCL11a Exon 4 + chr2: 60461189-60461214 GUGGCCGCGCUUAUGCUUC 725 UCGCCC 53335_4_173 BCL11a Exon 4 + chr2: 60461195-60461220 GCGCUUAUGCUUCUCGCCC 726 AGGACC 53335_4_174 BCL11a Exon 4 + chr2: 60461198-60461223 CUUAUGCUUCUCGCCCAGG 727 ACCUGG 53335_4_175 BCL11a Exon 4 + chr2: 60461202-60461227 UGCUUCUCGCCCAGGACCU 728 GGUGGA 53335_4_176 BCL11a Exon 4 + chr2: 60461223-60461248 UGGAAGGCCUCGCUGAAGU 729 GCUGCA 53335_4_177 BCL11a Exon 4 + chr2: 60461253-60461278 CUGAGCACCAUGCCCUGCA 730 UGACGU 53335_4_178 BCL11a Exon 4 + chr2: 60461254-60461279 UGAGCACCAUGCCCUGCAU 731 GACGUC 53335_4_179 BCL11a Exon 4 + chr2: 60461258-60461283 CACCAUGCCCUGCAUGACG 732 UCGGGC 53335_4_180 BCL11a Exon 4 + chr2: 60461259-60461284 ACCAUGCCCUGCAUGACGU 733 CGGGCA 53335_4_181 BCL11a Exon 4 + chr2: 60461264-60461289 GCCCUGCAUGACGUCGGGC 734 AGGGCG 53335_4_182 BCL11a Exon 4 + chr2: 60461312-60461337 GACCGCGCCCCGCGAGCUG 735 UUCUCG 53335_4_183 BCL11a Exon 4 + chr2: 60461315-60461340 CGCGCCCCGCGAGCUGUUC 736 UCGUGG 53335_4_184 BCL11a Exon 4 + chr2: 60461330-60461355 GUUCUCGUGGUGGCGCGCC 737 GCCUCC 53335_4_185 BCL11a Exon 4 + chr2: 60461446-60461471 CCUCUUCCUCCUCGUCCCCG 738 UUCUC 53335_4_186 BCL11a Exon 4 + chr2: 60461447-60461472 CUCUUCCUCCUCGUCCCCG 739 UUCUCC 53335_4_187 BCL11a Exon 4 + chr2: 60461453-60461478 CUCCUCGUCCCCGUUCUCC 740 GGGAUC 53335_4_188 BCL11a Exon 4 + chr2: 60461457-60461482 UCGUCCCCGUUCUCCGGGA 741 UCAGGU 53335_4_189 BCL11a Exon 4 + chr2: 60461458-60461483 CGUCCCCGUUCUCCGGGAU 742 CAGGUU 53335_4_190 BCL11a Exon 4 + chr2: 60461459-60461484 GUCCCCGUUCUCCGGGAUC 743 AGGUUG 53335_4_191 BCL11a Exon 4 + chr2: 60461481-60461506 UUGGGGUCGUUCUCGCUCU 744 UGAACU 53335_4_192 BCL11a Exon 4 + chr2: 60461490-60461515 UUCUCGCUCUUGAACUUGG 745 CCACCA 53335_4_193 BCL11a Exon 4 + chr2: 60461508-60461533 GCCACCACGGACUUGAGCG 746 CGCUGC 53335_4_194 BCL11a Exon 4 + chr2: 60461529-60461554 CUGCUGGCGCUGCCCACCA 747 AGUCGC 53335_4_195 BCL11a Exon 4 + chr2: 60461535-60461560 GCGCUGCCCACCAAGUCGC 748 UGGUGC 53335_4_196 BCL11a Exon 4 + chr2: 60461536-60461561 CGCUGCCCACCAAGUCGCU 749 GGUGCC 53335_4_197 BCL11a Exon 4 + chr2: 60461542-60461567 CCACCAAGUCGCUGGUGCC 750 GGGUUC 53335_4_198 BCL11a Exon 4 + chr2: 60461543-60461568 CACCAAGUCGCUGGUGCCG 751 GGUUCC 53335_4_199 BCL11a Exon 4 + chr2: 60461544-60461569 ACCAAGUCGCUGGUGCCGG 752 GUUCCG 53335_4_200 BCL11a Exon 4 + chr2: 60461550-60461575 UCGCUGGUGCCGGGUUCCG 753 GGGAGC 53335_4_201 BCL11a Exon 4 + chr2: 60461553-60461578 CUGGUGCCGGGUUCCGGGG 754 AGCUGG 53335_4_202 BCL11a Exon 4 + chr2: 60461556-60461581 GUGCCGGGUUCCGGGGAGC 755 UGGCGG 53335_4_203 BCL11a Exon 4 + chr2: 60461571-60461596 GAGCUGGCGGUGGAGAGAC 756 CGUCGU 53335_4_204 BCL11a Exon 4 + chr2: 60461586-60461611 AGACCGUCGUCGGACUUGA 757 CCGUCA 53335_4_205 BCL11a Exon 4 + chr2: 60461587-60461612 GACCGUCGUCGGACUUGAC 758 CGUCAU 53335_4_206 BCL11a Exon 4 + chr2: 60461588-60461613 ACCGUCGUCGGACUUGACC 759 GUCAUG 53335_4_207 BCL11a Exon 4 + chr2: 60461589-60461614 CCGUCGUCGGACUUGACCG 760 UCAUGG 53335_4_208 BCL11a Exon 4 + chr2: 60461618-60461643 CGAUUUGUGCAUGUGCGUC 761 UUCAUG 53335_4_209 BCL11a Exon 4 + chr2: 60461634-60461659 GUCUUCAUGUGGCGCUUCA 762 GCUUGC 53335_4_210 BCL11a Exon 4 + chr2: 60461639-60461664 CAUGUGGCGCUUCAGCUUG 763 CUGGCC 53335_4_211 BCL11a Exon 4 + chr2: 60461640-60461665 AUGUGGCGCUUCAGCUUGC 764 UGGCCU 53335_4_212 BCL11a Exon 4 + chr2: 60461651-60461676 CAGCUUGCUGGCCUGGGUG 765 CACGCG 53335_4_213 BCL11a Exon 4 + chr2: 60461660-60461685 GGCCUGGGUGCACGCGUGG 766 UCGCAC 53335_4_214 BCL11a Exon 4 + chr2: 60461673-60461698 GCGUGGUCGCACAGGUUGC 767 ACUUGU 53335_4_215 BCL11a Exon 4 + chr2: 60461674-60461699 CGUGGUCGCACAGGUUGCA 768 CUUGUA 53335_4_216 BCL11a Exon 4 + chr2: 60461690-60461715 GCACUUGUAGGGCUUCUCG 769 CCCGUG 53335_4_217 BCL11a Exon 4 + chr2: 60461699-60461724 GGGCUUCUCGCCCGUGUGG 770 CUGCGC 53335_4_218 BCL11a Exon 4 + chr2: 60461711-60461736 CGUGUGGCUGCGCCGGUGC 771 ACCACC 53335_4_219 BCL11a Exon 4 + chr2: 60461757-60461782 GUCUUGCCGCAGAACUCGC 772 AUGACU 53335_4_220 BCL11a Exon 4 + chr2: 60461767-60461792 AGAACUCGCAUGACUUGGA 773 CUUGAC 53335_4_221 BCL11a Exon 4 + chr2: 60461768-60461793 GAACUCGCAUGACUUGGAC 774 UUGACC 53335_4_222 BCL11a Exon 4 + chr2: 60461769-60461794 AACUCGCAUGACUUGGACU 775 UGACCG 53335_4_223 BCL11a Exon 4 + chr2: 60461770-60461795 ACUCGCAUGACUUGGACUU 776 GACCGG 53335_4_224 BCL11a Exon 4 + chr2: 60461774-60461799 GCAUGACUUGGACUUGACC 777 GGGGGC 53335_4_225 BCL11a Exon 4 + chr2: 60461775-60461800 CAUGACUUGGACUUGACCG 778 GGGGCU 53335_4_226 BCL11a Exon 4 + chr2: 60461778-60461803 GACUUGGACUUGACCGGGG 779 GCUGGG 53335_4_227 BCL11a Exon 4 + chr2: 60461779-60461804 ACUUGGACUUGACCGGGGG 780 CUGGGA 53335_4_228 BCL11a Exon 4 + chr2: 60461782-60461807 UGGACUUGACCGGGGGCUG 781 GGAGGG 53335_4_229 BCL11a Exon 4 + chr2: 60461785-60461810 ACUUGACCGGGGGCUGGGA 782 GGGAGG 53335_4_230 BCL11a Exon 4 + chr2: 60461786-60461811 CUUGACCGGGGGCUGGGAG 783 GGAGGA 53335_4_231 BCL11a Exon 4 + chr2: 60461787-60461812 UUGACCGGGGGCUGGGAGG 784 GAGGAG 53335_4_232 BCL11a Exon 4 + chr2: 60461790-60461815 ACCGGGGGCUGGGAGGGAG 785 GAGGGG 53335_4_233 BCL11a Exon 4 + chr2: 60461800-60461825 GGGAGGGAGGAGGGGCGGA 786 UUGCAG 53335_4_234 BCL11a Exon 4 + chr2: 60461803-60461828 AGGGAGGAGGGGCGGAUUG 787 CAGAGG 53335_4_235 BCL11a Exon 4 + chr2: 60461804-60461829 GGGAGGAGGGGCGGAUUGC 788 AGAGGA 53335_4_236 BCL11a Exon 4 + chr2: 60461807-60461832 AGGAGGGGCGGAUUGCAGA 789 GGAGGG 53335_4_237 BCL11a Exon 4 + chr2: 60461808-60461833 GGAGGGGCGGAUUGCAGAG 790 GAGGGA 53335_4_238 BCL11a Exon 4 + chr2: 60461809-60461834 GAGGGGCGGAUUGCAGAGG 791 AGGGAG 53335_4_239 BCL11a Exon 4 + chr2: 60461810-60461835 AGGGGCGGAUUGCAGAGGA 792 GGGAGG 53335_4_240 BCL11a Exon 4 + chr2: 60461811-60461836 GGGGCGGAUUGCAGAGGAG 793 GGAGGG 53335_4_241 BCL11a Exon 4 + chr2: 60461812-60461837 GGGCGGAUUGCAGAGGAGG 794 GAGGGG 53335_4_242 BCL11a Exon 4 + chr2: 60461822-60461847 CAGAGGAGGGAGGGGGGGC 795 GUCGCC 53335_4_243 BCL11a Exon 4 + chr2: 60461826-60461851 GGAGGGAGGGGGGGCGUCG 796 CCAGGA 53335_4_244 BCL11a Exon 4 + chr2: 60461827-60461852 GAGGGAGGGGGGGCGUCGC 797 CAGGAA 53335_4_245 BCL11a Exon 4 + chr2: 60461830-60461855 GGAGGGGGGGCGUCGCCAG 798 GAAGGG 53335_4_246 BCL11a Exon 4 + chr2: 60461842-60461867 UCGCCAGGAAGGGCGGCUU 799 GCUACC 53335_4_247 BCL11a Exon 4 + chr2: 60461846-60461871 CAGGAAGGGCGGCUUGCUA 800 CCUGGC 53335_4_248 BCL11a Exon 4 + chr2: 60461851-60461876 AGGGCGGCUUGCUACCUGG 801 CUGGAA 53335_4_249 BCL11a Exon 4 + chr2: 60461872-60461897 GGAAUGGUUGCAGUAACCU 802 UUGCAU 53335_4_250 BCL11a Exon 4 + chr2: 60461873-60461898 GAAUGGUUGCAGUAACCUU 803 UGCAUA 53335_4_251 BCL11a Exon 4 + chr2: 60461877-60461902 GGUUGCAGUAACCUUUGCA 804 UAGGGC 53335_4_252 BCL11a Exon 4 + chr2: 60461878-60461903 GUUGCAGUAACCUUUGCAU 805 AGGGCU 53335_4_253 BCL11a Exon 4 + chr2: 60461882-60461907 CAGUAACCUUUGCAUAGGG 806 CUGGGC 53335_4_254 BCL11a Exon 4 + chr2: 60461887-60461912 ACCUUUGCAUAGGGCUGGG 807 CCGGCC 53335_4_255 BCL11a Exon 4 + chr2: 60461888-60461913 CCUUUGCAUAGGGCUGGGC 808 CGGCCU 53335_4_256 BCL11a Exon 4 + chr2: 60461889-60461914 CUUUGCAUAGGGCUGGGCC 809 GGCCUG 53335_4_257 BCL11a Exon 4 + chr2: 60461896-60461921 UAGGGCUGGGCCGGCCUGG 810 GGACAG 53335_4_258 BCL11a Exon 4 + chr2: 60461899-60461924 GGCUGGGCCGGCCUGGGGA 811 CAGCGG 53335_4_259 BCL11a Exon 4 + chr2: 60461900-60461925 GCUGGGCCGGCCUGGGGAC 812 AGCGGU 53335_4_260 BCL11a Exon 4 + chr2: 60461949-60461974 UCUCUAAGUCUCCUAGAGA 813 AAUCCA 53335_4_261 BCL11a Exon 4 + chr2: 60461952-60461977 CUAAGUCUCCUAGAGAAAU 814 CCAUGG 53335_4_262 BCL11a Exon 4 + chr2: 60461953-60461978 UAAGUCUCCUAGAGAAAUC 815 CAUGGC 53335_4_263 BCL11a Exon 4 + chr2: 60461956-60461981 GUCUCCUAGAGAAAUCCAU 816 GGCGGG 53335_4_264 BCL11a Exon 4 + chr2: 60461971-60461996 CCAUGGCGGGAGGCUCCAU 817 AGCCAU 53335_4_265 BCL11a Exon 4 + chr2: 60461997-60462022 GGAUUCAACCGCAGCACCC 818 UGUCAA 53335_4_266 BCL11a Exon 4 + chr2: 60462004-60462029 ACCGCAGCACCCUGUCAAA 819 GGCACU 53335_4_267 BCL11a Exon 4 + chr2: 60462005-60462030 CCGCAGCACCCUGUCAAAG 820 GCACUC 53335_4_268 BCL11a Exon 4 + chr2: 60462011-60462036 CACCCUGUCAAAGGCACUC 821 GGGUGA 53335_4_269 BCL11a Exon 4 + chr2: 60462012-60462037 ACCCUGUCAAAGGCACUCG 822 GGUGAU 53335_4_270 BCL11a Exon 4 + chr2: 60462015-60462040 CUGUCAAAGGCACUCGGGU 823 GAUGGG 53335_4_271 BCL11a Exon 4 + chr2: 60462020-60462045 AAAGGCACUCGGGUGAUGG 824 GUGGCC 53335_4_272 BCL11a Exon 4 + chr2: 60462021-60462046 AAGGCACUCGGGUGAUGGG 825 UGGCCA 53335_4_273 BCL11a Exon 4 + chr2: 60462041-60462066 GGCCAGGGCCAUCUCUUCC 826 GCCCCC 53335_4_274 BCL11a Exon 4 + chr2: 60462053-60462078 CUCUUCCGCCCCCAGGCGC 827 UCUAUG 53335_4_275 BCL11a Exon 4 + chr2: 60462056-60462081 UUCCGCCCCCAGGCGCUCU 828 AUGCGG 53335_4_276 BCL11a Exon 4 + chr2: 60462057-60462082 UCCGCCCCCAGGCGCUCUA 829 UGCGGU 53335_4_277 BCL11a Exon 4 + chr2: 60462058-60462083 CCGCCCCCAGGCGCUCUAU 830 GCGGUG 53335_4_278 BCL11a Exon 4 + chr2: 60462059-60462084 CGCCCCCAGGCGCUCUAUG 831 CGGUGG 53335_4_279 BCL11a Exon 4 + chr2: 60462076-60462101 UGCGGUGGGGGUCCAAGUG 832 AUGUCU 53335_4_280 BCL11a Exon 4 + chr2: 60462079-60462104 GGUGGGGGUCCAAGUGAUG 833 UCUCGG 53335_4_281 BCL11a Exon 4 + chr2: 60462082-60462107 GGGGGUCCAAGUGAUGUCU 834 CGGUGG 53335_4_282 BCL11a Exon 4 + chr2: 60462092-60462117 GUGAUGUCUCGGUGGUGGA 835 CUAAAC 53335_4_283 BCL11a Exon 4 + chr2: 60462093-60462118 UGAUGUCUCGGUGGUGGAC 836 UAAACA 53335_4_284 BCL11a Exon 4 + chr2: 60462094-60462119 GAUGUCUCGGUGGUGGACU 837 AAACAG 53335_4_285 BCL11a Exon 4 + chr2: 60462095-60462120 AUGUCUCGGUGGUGGACUA 838 AACAGG 53335_4_286 BCL11a Exon 4 + chr2: 60462096-60462121 UGUCUCGGUGGUGGACUAA 839 ACAGGG 53335_4_287 BCL11a Exon 4 + chr2: 60462097-60462122 GUCUCGGUGGUGGACUAAA 840 CAGGGG 53335_4_288 BCL11a Exon 4 + chr2: 60462102-60462127 GGUGGUGGACUAAACAGGG 841 GGGGAG 53335_4_289 BCL11a Exon 4 + chr2: 60462103-60462128 GUGGUGGACUAAACAGGGG 842 GGGAGU 53335_4_290 BCL11a Exon 4 + chr2: 60462106-60462131 GUGGACUAAACAGGGGGGG 843 AGUGGG 53335_4_291 BCL11a Exon 4 + chr2: 60462125-60462150 AGUGGGUGGAAAGCGCCCU 844 UCUGCC 53335_4_292 BCL11a Exon 4 + chr2: 60462129-60462154 GGUGGAAAGCGCCCUUCUG 845 CCAGGC 53335_4_293 BCL11a Exon 4 + chr2: 60462154-60462179 CGGAAGCCUCUCUCGAUAC 846 UGAUCC 53335_4_294 BCL11a Exon 4 + chr2: 60462167-60462192 CGAUACUGAUCCUGGUAUU 847 CUUAGC 53335_4_295 BCL11a Exon 4 + chr2: 60462174-60462199 GAUCCUGGUAUUCUUAGCA 848 GGUUAA 53335_4_296 BCL11a Exon 4 + chr2: 60462175-60462200 AUCCUGGUAUUCUUAGCAG 849 GUUAAA 53335_4_297 BCL11a Exon 4 + chr2: 60462176-60462201 UCCUGGUAUUCUUAGCAGG 850 UUAAAG 53335_4_298 BCL11a Exon 4 + chr2: 60462203-60462228 GUUAUUGUCUGCAAUAUGA 851 AUCCCA 53335_4_299 BCL11a Exon 4 + chr2: 60462208-60462233 UGUCUGCAAUAUGAAUCCC 852 AUGGAG 53335_4_300 BCL11a Exon 4 + chr2: 60462211-60462236 CUGCAAUAUGAAUCCCAUG 853 GAGAGG 53335_4_301 BCL11a Exon 4 + chr2: 60462215-60462240 AAUAUGAAUCCCAUGGAGA 854 GGUGGC 53335_4_302 BCL11a Exon 4 + chr2: 60462216-60462241 AUAUGAAUCCCAUGGAGAG 855 GUGGCU 53335_4_303 BCL11a Exon 4 + chr2: 60462220-60462245 GAAUCCCAUGGAGAGGUGG 856 CUGGGA 53335_4_304 BCL11a Exon 4 + chr2: 60462244-60462269 AAGGACAUUCUGCACCUAG 857 UCCUGA 53335_4_305 BCL11a Exon 4 + chr2: 60462245-60462270 AGGACAUUCUGCACCUAGU 858 CCUGAA 53335_4_306 BCL11a Exon 4 + chr2: 60462259-60462284 CUAGUCCUGAAGGGAUACC 859 AACCCG 53335_4_307 BCL11a Exon 4 + chr2: 60462260-60462285 UAGUCCUGAAGGGAUACCA 860 ACCCGC 53335_4_308 BCL11a Exon 4 + chr2: 60462261-60462286 AGUCCUGAAGGGAUACCAA 861 CCCGCG 53335_4_309 BCL11a Exon 4 + chr2: 60462266-60462291 UGAAGGGAUACCAACCCGC 862 GGGGUC 53335_4_310 BCL11a Exon 4 + chr2: 60462267-60462292 GAAGGGAUACCAACCCGCG 863 GGGUCA 53335_4_311 BCL11a Exon 4 + chr2: 60462268-60462293 AAGGGAUACCAACCCGCGG 864 GGUCAG 53335_4_312 BCL11a Exon 4 + chr2: 60462345-60462370 GCGUGUUGCAAGAGAAACC 865 AUGCAC 53335_4_313 BCL11a Exon 4 + chr2: 60462352-60462377 GCAAGAGAAACCAUGCACU 866 GGUGAA 53335_4_314 BCL11a Exon 4 + chr2: 60462384-60462409 UUGCAAGUUGUACAUGUGU 867 AGCUGC 53335_4_315 BCL11a Exon 4 + chr2: 60462385-60462410 UGCAAGUUGUACAUGUGUA 868 GCUGCU 53335_4_316 BCL11a Exon 4 − chr2: 60457269-60457294 GGAAAAACCACUGUCUGUG 869 UUUUUU 53335_4_317 BCL11a Exon 4 − chr2: 60457295-60457320 GUUUCUGGUCUUUGUUAAG 870 UUCUAU 53335_4_318 BCL11a Exon 4 − chr2: 60457315-60457340 CCUGGCUUUUUAUUGUAUU 871 UGUUUC 53335_4_319 BCL11a Exon 4 − chr2: 60457338-60457363 AAGAUGACCAAAGGUCAUU 872 ACAACC 53335_4_320 BCL11a Exon 4 − chr2: 60457352-60457377 AAAAAAAAAAAUAAAAGAU 873 GACCAA 53335_4_321 BCL11a Exon 4 − chr2: 60457415-60457440 UGCUUAUGUGCCCUGUUCA 874 AAACAG 53335_4_322 BCL11a Exon 4 − chr2: 60457459-60457484 AACUUGAAAUUUUAUCUUU 875 UACUAU 53335_4_323 BCL11a Exon 4 − chr2: 60457460-60457485 UAACUUGAAAUUUUAUCUU 876 UUACUA 53335_4_324 BCL11a Exon 4 − chr2: 60457522-60457547 AUGGCAAUGCAGAAUAUUU 877 UGUUAU 53335_4_325 BCL11a Exon 4 − chr2: 60457546-60457571 GCUUUAGUCAAUACUUUUU 878 UGUAAA 53335_4_326 BCL11a Exon 4 − chr2: 60457613-60457638 ACUAAAUGGUGCUUUAUAU 879 UUAGAU 53335_4_327 BCL11a Exon 4 − chr2: 60457632-60457657 GUUUUUUUCAUUGCCAAAA 880 ACUAAA 53335_4_328 BCL11a Exon 4 − chr2: 60457786-60457811 AUGCAGUACUGCAAGCUAA 881 UAACGU 53335_4_329 BCL11a Exon 4 − chr2: 60457858-60457883 AAUGUCACAUGGAUGGCUG 882 UCAUAG 53335_4_330 BCL11a Exon 4 − chr2: 60457859-60457884 GAAUGUCACAUGGAUGGCU 883 GUCAUA 53335_4_331 BCL11a Exon 4 − chr2: 60457860-60457885 AGAAUGUCACAUGGAUGGC 884 UGUCAU 53335_4_332 BCL11a Exon 4 − chr2: 60457870-60457895 GGAGCCUGCUAGAAUGUCA 885 CAUGGA 53335_4_333 BCL11a Exon 4 − chr2: 60457874-60457899 UGGGGGAGCCUGCUAGAAU 886 GUCACA 53335_4_334 BCL11a Exon 4 − chr2: 60457896-60457921 GAGAAGCCAUAUAAUGGCG 887 GUUUGG 53335_4_335 BCL11a Exon 4 − chr2: 60457897-60457922 UGAGAAGCCAUAUAAUGGC 888 GGUUUG 53335_4_336 BCL11a Exon 4 − chr2: 60457898-60457923 AUGAGAAGCCAUAUAAUGG 889 CGGUUU 53335_4_337 BCL11a Exon 4 − chr2: 60457899-60457924 GAUGAGAAGCCAUAUAAUG 890 GCGGUU 53335_4_338 BCL11a Exon 4 − chr2: 60457904-60457929 UUACAGAUGAGAAGCCAUA 891 UAAUGG 53335_4_339 BCL11a Exon 4 − chr2: 60457907-60457932 ACAUUACAGAUGAGAAGCC 892 AUAUAA 53335_4_340 BCL11a Exon 4 − chr2: 60457999-60458024 CCACAGUAUAUUUUUUUAA 893 UUUGGC 53335_4_341 BCL11a Exon 4 − chr2: 60458003-60458028 GCUGCCACAGUAUAUUUUU 894 UUAAUU 53335_4_342 BCL11a Exon 4 − chr2: 60458030-60458055 UUUUGGUAGUGGAAAAAAA 895 AAAGAC 53335_4_343 BCL11a Exon 4 − chr2: 60458046-60458071 GGUAUCAAUGUACCUUUUU 896 UGGUAG 53335_4_344 BCL11a Exon 4 − chr2: 60458052-60458077 UUAAAAGGUAUCAAUGUAC 897 CUUUUU 53335_4_345 BCL11a Exon 4 − chr2: 60458072-60458097 UUUAACUGUUGCUUGUUCU 898 CUUAAA 53335_4_346 BCL11a Exon 4 − chr2: 60458130-60458155 UUGAAUUAAAUGUUCAUCU 899 AGUGUU 53335_4_347 BCL11a Exon 4 − chr2: 60458161-60458186 UGGUCUUUUUUCUGUAUUU 900 CUAGAA 53335_4_348 BCL11a Exon 4 − chr2: 60458186-60458211 UGAUUCCUAUGCUAAAAUA 901 CAUUUA 53335_4_349 BCL11a Exon 4 − chr2: 60458231-60458256 UUAAGAUUAUAUAGUACUU 902 AAAUAU 53335_4_350 BCL11a Exon 4 − chr2: 60458260-60458285 AAAAAAAAAAACAUACAUU 903 GGGGAA 53335_4_351 BCL11a Exon 4 − chr2: 60458265-60458290 UUGUAAAAAAAAAAAACAU 904 ACAUUG 53335_4_352 BCL11a Exon 4 − chr2: 60458266-60458291 GUUGUAAAAAAAAAAAACA 905 UACAUU 53335_4_353 BCL11a Exon 4 − chr2: 60458267-60458292 GGUUGUAAAAAAAAAAAAC 906 AUACAU 53335_4_354 BCL11a Exon 4 − chr2: 60458293-60458318 AUGCCUUGGAUACACACCG 907 CUCUUC 53335_4_355 BCL11a Exon 4 − chr2: 60458312-60458337 AAAUGGUAGUGGAAAUUCU 908 AUGCCU 53335_4_356 BCL11a Exon 4 − chr2: 60458328-60458353 CUUGUUAUCCAUUUAAAAA 909 UGGUAG 53335_4_357 BCL11a Exon 4 − chr2: 60458334-60458359 ACAAGACUUGUUAUCCAUU 910 UAAAAA 53335_4_358 BCL11a Exon 4 − chr2: 60458366-60458391 GCAUUUUAGGGUUCCAUUG 911 UCUUGG 53335_4_359 BCL11a Exon 4 − chr2: 60458369-60458394 ACUGCAUUUUAGGGUUCCA 912 UUGUCU 53335_4_360 BCL11a Exon 4 − chr2: 60458383-60458408 AUGUUUAGGGGGGAACUGC 913 AUUUUA 53335_4_361 BCL11a Exon 4 − chr2: 60458384-60458409 UAUGUUUAGGGGGGAACUG 914 CAUUUU 53335_4_362 BCL11a Exon 4 − chr2: 60458398-60458423 AAAAAACACUUCAUUAUGU 915 UUAGGG 53335_4_363 BCL11a Exon 4 − chr2: 60458399-60458424 UAAAAAACACUUCAUUAUG 916 UUUAGG 53335_4_364 BCL11a Exon 4 − chr2: 60458400-60458425 UUAAAAAACACUUCAUUAU 917 GUUUAG 53335_4_365 BCL11a Exon 4 − chr2: 60458401-60458426 UUUAAAAAACACUUCAUUA 918 UGUUUA 53335_4_366 BCL11a Exon 4 − chr2: 60458402-60458427 UUUUAAAAAACACUUCAUU 919 AUGUUU 53335_4_367 BCL11a Exon 4 − chr2: 60458478-60458503 UGAUUGCUUUCGCUUCUAC 920 AGUGCA 53335_4_368 BCL11a Exon 4 − chr2: 60458535-60458560 GACGCAACAUUGCAAGCGC 921 UGUGAA 53335_4_369 BCL11a Exon 4 − chr2: 60458562-60458587 UACUUGACUAUUGAGCUUA 922 CUUACU 53335_4_370 BCL11a Exon 4 − chr2: 60458634-60458659 AAAAAAAUUGAACACAAUC 923 UCAUUG 53335_4_371 BCL11a Exon 4 − chr2: 60458682-60458707 UCCCAGUUUACAGGUCUAU 924 ACUUAA 53335_4_372 BCL11a Exon 4 − chr2: 60458683-60458708 UUCCCAGUUUACAGGUCUA 925 UACUUA 53335_4_373 BCL11a Exon 4 − chr2: 60458696-60458721 GCACUGUACAAUUUUCCCA 926 GUUUAC 53335_4_374 BCL11a Exon 4 − chr2: 60458734-60458759 GAGUAUAAAAUAAACCUGC 927 UCAGAU 53335_4_375 BCL11a Exon 4 − chr2: 60458764-60458789 AUCUUUUCUCUAAUCAGAG 928 AUACAG 53335_4_376 BCL11a Exon 4 − chr2: 60458829-60458854 AAUAAAAGCUAGCAUCUGC 929 CCCAGU 53335_4_377 BCL11a Exon 4 − chr2: 60458897-60458922 UGUGCUAUUUGUGUUAACA 930 UGGAAG 53335_4_378 BCL11a Exon 4 − chr2: 60458903-60458928 ACACUGUGUGCUAUUUGUG 931 UUAACA 53335_4_379 BCL11a Exon 4 − chr2: 60459085-60459110 ACUAUUUGCCAUUUAAAAC 932 UAGAAC 53335_4_380 BCL11a Exon 4 − chr2: 60459114-60459139 AAUAAUAUGAUUUAUUAGC 933 ACAACG 53335_4_381 BCL11a Exon 4 − chr2: 60459152-60459177 AGGCUGACAAUAAGGUUUG 934 ACAGAG 53335_4_382 BCL11a Exon 4 − chr2: 60459153-60459178 GAGGCUGACAAUAAGGUUU 935 GACAGA 53335_4_383 BCL11a Exon 4 − chr2: 60459154-60459179 AGAGGCUGACAAUAAGGUU 936 UGACAG 53335_4_384 BCL11a Exon 4 − chr2: 60459165-60459190 UAUUGAAAGGAAGAGGCUG 937 ACAAUA 53335_4_385 BCL11a Exon 4 − chr2: 60459177-60459202 CCUUGUAUACCAUAUUGAA 938 AGGAAG 53335_4_386 BCL11a Exon 4 − chr2: 60459183-60459208 UUAAGACCUUGUAUACCAU 939 AUUGAA 53335_4_387 BCL11a Exon 4 − chr2: 60459229-60459254 GAUCCAGAUCUACUUGGUU 940 GUCAAG 53335_4_388 BCL11a Exon 4 − chr2: 60459240-60459265 CAAAAGAAAUAGAUCCAGA 941 UCUACU 53335_4_389 BCL11a Exon 4 − chr2: 60459271-60459296 UUUAAUAAUGUCUUUUUAA 942 AAAUAC 53335_4_390 BCL11a Exon 4 − chr2: 60459323-60459348 UGGAACGCAAUUAAAUACA 943 CUAGUA 53335_4_391 BCL11a Exon 4 − chr2: 60459348-60459373 UUGAAUGUGUAAUGUGCAA 944 AAGCCC 53335_4_392 BCL11a Exon 4 − chr2: 60459418-60459443 CUCCUGGUGAGAGCUUAAA 945 AGAAAU 53335_4_393 BCL11a Exon 4 − chr2: 60459419-60459444 GCUCCUGGUGAGAGCUUAA 946 AAGAAA 53335_4_394 BCL11a Exon 4 − chr2: 60459439-60459464 ACCAGUAUAAAAGCUACUU 947 UGCUCC 53335_4_395 BCL11a Exon 4 − chr2: 60459547-60459572 UUCUAUAUUGUAUUUCUCA 948 CAACAA 53335_4_396 BCL11a Exon 4 − chr2: 60459588-60459613 AGCAUUGGGUGAGGUAAUA 949 AACCUU 53335_4_397 BCL11a Exon 4 − chr2: 60459602-60459627 UUGUAGCUUAAUUCAGCAU 950 UGGGUG 53335_4_398 BCL11a Exon 4 − chr2: 60459607-60459632 UAAACUUGUAGCUUAAUUC 951 AGCAUU 53335_4_399 BCL11a Exon 4 − chr2: 60459608-60459633 AUAAACUUGUAGCUUAAUU 952 CAGCAU 53335_4_400 BCL11a Exon 4 − chr2: 60459651-60459676 CUUGGAUCUAUUAAAACCA 953 CAUCGA 53335_4_401 BCL11a Exon 4 − chr2: 60459674-60459699 AUUUGGUUUUAAAAUAUGA 954 GUGCCU 53335_4_402 BCL11a Exon 4 − chr2: 60459696-60459721 AACAGAACAAGUUUAUUCU 955 AUCAUU 53335_4_403 BCL11a Exon 4 − chr2: 60459749-60459774 UGUAUCAAUUGGAAAGGAA 956 GAAAAA 53335_4_404 BCL11a Exon 4 − chr2: 60459760-60459785 AAAGGGUUAAAUGUAUCAA 957 UUGGAA 53335_4_405 BCL11a Exon 4 − chr2: 60459765-60459790 UCUCUAAAGGGUUAAAUGU 958 AUCAAU 53335_4_406 BCL11a Exon 4 − chr2: 60459782-60459807 UAUGAGCUAAAUGUCUGUC 959 UCUAAA 53335_4_407 BCL11a Exon 4 − chr2: 60459783-60459808 CUAUGAGCUAAAUGUCUGU 960 CUCUAA 53335_4_408 BCL11a Exon 4 − chr2: 60459855-60459880 UAACGUGAGGAGGAAAAAC 961 AGUCUU 53335_4_409 BCL11a Exon 4 − chr2: 60459870-60459895 UACAGUUUUAUUUUAUAAC 962 GUGAGG 53335_4_410 BCL11a Exon 4 − chr2: 60459873-60459898 AUGUACAGUUUUAUUUUAU 963 AACGUG 53335_4_411 BCL11a Exon 4 − chr2: 60460023-60460048 CUUAGACAGCAUGUAUGGU 964 AUGUUA 53335_4_412 BCL11a Exon 4 − chr2: 60460033-60460058 UUUUUUUAAACUUAGACAG 965 CAUGUA 53335_4_413 BCL11a Exon 4 − chr2: 60460130-60460155 ACCGUUUGAAUGCAUGAUC 966 UGUAUG 53335_4_414 BCL11a Exon 4 − chr2: 60460131-60460156 CACCGUUUGAAUGCAUGAU 967 CUGUAU 53335_4_415 BCL11a Exon 4 − chr2: 60460132-60460157 UCACCGUUUGAAUGCAUGA 968 UCUGUA 53335_4_416 BCL11a Exon 4 − chr2: 60460314-60460339 AUCGCCCUCCAGCCCCACUC 969 CCUGU 53335_4_417 BCL11a Exon 4 − chr2: 60460403-60460428 GAAUAAUGAUAUAAAAACU 970 GAAUAG 53335_4_418 BCL11a Exon 4 − chr2: 60460448-60460473 UACCCUGGAGAAACACAUG 971 AAAAAA 53335_4_419 BCL11a Exon 4 − chr2: 60460468-60460493 AUGCCUUUUAGCGUGUACA 972 GUACCC 53335_4_420 BCL11a Exon 4 − chr2: 60460522-60460547 AUGAAAACGCAUGGCCAGG 973 UGGGGA 53335_4_421 BCL11a Exon 4 − chr2: 60460526-60460551 GCACAUGAAAACGCAUGGC 974 CAGGUG 53335_4_422 BCL11a Exon 4 − chr2: 60460527-60460552 GGCACAUGAAAACGCAUGG 975 CCAGGU 53335_4_423 BCL11a Exon 4 − chr2: 60460528-60460553 AGGCACAUGAAAACGCAUG 976 GCCAGG 53335_4_424 BCL11a Exon 4 − chr2: 60460531-60460556 ACCAGGCACAUGAAAACGC 977 AUGGCC 53335_4_425 BCL11a Exon 4 − chr2: 60460536-60460561 AGCUCACCAGGCACAUGAA 978 AACGCA 53335_4_426 BCL11a Exon 4 − chr2: 60460553-60460578 CUGUGCCCAGAGUAGCAAG 979 CUCACC 53335_4_427 BCL11a Exon 4 − chr2: 60460610-60460635 CCACAGGAGAAGCCACACG 980 GGCGAA 53335_4_428 BCL11a Exon 4 − chr2: 60460617-60460642 UCACUGUCCACAGGAGAAG 981 CCACAC 53335_4_429 BCL11a Exon 4 − chr2: 60460618-60460643 CUCACUGUCCACAGGAGAA 982 GCCACA 53335_4_430 BCL11a Exon 4 − chr2: 60460631-60460656 GAACUGUAGCAAUCUCACU 983 GUCCAC 53335_4_431 BCL11a Exon 4 − chr2: 60460670-60460695 ACGCAGCGACACUUGUGAG 984 UACUGU 53335_4_432 BCL11a Exon 4 − chr2: 60460671-60460696 GACGCAGCGACACUUGUGA 985 GUACUG 53335_4_433 BCL11a Exon 4 − chr2: 60460701-60460726 GCCCGGGCAGGCCCAGCUC 986 AAAAGA 53335_4_434 BCL11a Exon 4 − chr2: 60460702-60460727 GGCCCGGGCAGGCCCAGCU 987 CAAAAG 53335_4_435 BCL11a Exon 4 − chr2: 60460718-60460743 CCAUAUUAGUGGUCCGGGC 988 CCGGGC 53335_4_436 BCL11a Exon 4 − chr2: 60460722-60460747 CGCCCCAUAUUAGUGGUCC 989 GGGCCC 53335_4_437 BCL11a Exon 4 − chr2: 60460723-60460748 ACGCCCCAUAUUAGUGGUC 990 CGGGCC 53335_4_438 BCL11a Exon 4 − chr2: 60460728-60460753 GGAGCACGCCCCAUAUUAG 991 UGGUCC 53335_4_439 BCL11a Exon 4 − chr2: 60460729-60460754 GGGAGCACGCCCCAUAUUA 992 GUGGUC 53335_4_440 BCL11a Exon 4 − chr2: 60460734-60460759 GUGGAGGGAGCACGCCCCA 993 UAUUAG 53335_4_441 BCL11a Exon 4 − chr2: 60460754-60460779 GGGGCGCAGCGGCACGGGA 994 AGUGGA 53335_4_442 BCL11a Exon 4 − chr2: 60460755-60460780 CGGGGCGCAGCGGCACGGG 995 AAGUGG 53335_4_443 BCL11a Exon 4 − chr2: 60460758-60460783 UCUCGGGGCGCAGCGGCAC 996 GGGAAG 53335_4_444 BCL11a Exon 4 − chr2: 60460764-60460789 GAGGGAUCUCGGGGCGCAG 997 CGGCAC 53335_4_445 BCL11a Exon 4 − chr2: 60460765-60460790 GGAGGGAUCUCGGGGCGCA 998 GCGGCA 53335_4_446 BCL11a Exon 4 − chr2: 60460770-60460795 UGGACGGAGGGAUCUCGGG 999 GCGCAG 53335_4_447 BCL11a Exon 4 − chr2: 60460778-60460803 CGGGGAGCUGGACGGAGGG 1000 AUCUCG 53335_4_448 BCL11a Exon 4 − chr2: 60460779-60460804 CCGGGGAGCUGGACGGAGG 1001 GAUCUC 53335_4_449 BCL11a Exon 4 − chr2: 60460780-60460805 CCCGGGGAGCUGGACGGAG 1002 GGAUCU 53335_4_450 BCL11a Exon 4 − chr2: 60460787-60460812 CACACCGCCCGGGGAGCUG 1003 GACGGA 53335_4_451 BCL11a Exon 4 − chr2: 60460788-60460813 CCACACCGCCCGGGGAGCU 1004 GGACGG 53335_4_452 BCL11a Exon 4 − chr2: 60460791-60460816 UCUCCACACCGCCCGGGGA 1005 GCUGGA 53335_4_453 BCL11a Exon 4 − chr2: 60460795-60460820 CGCUUCUCCACACCGCCCG 1006 GGGAGC 53335_4_454 BCL11a Exon 4 − chr2: 60460801-60460826 AGUUUGCGCUUCUCCACAC 1007 CGCCCG 53335_4_455 BCL11a Exon 4 − chr2: 60460802-60460827 GAGUUUGCGCUUCUCCACA 1008 CCGCCC 53335_4_456 BCL11a Exon 4 − chr2: 60460803-60460828 GGAGUUUGCGCUUCUCCAC 1009 ACCGCC 53335_4_457 BCL11a Exon 4 − chr2: 60460829-60460854 CUCGUCGGAGCACUCCUCG 1010 GAGAAC 53335_4_458 BCL11a Exon 4 − chr2: 60460830-60460855 CCUCGUCGGAGCACUCCUC 1011 GGAGAA 53335_4_459 BCL11a Exon 4 − chr2: 60460837-60460862 UUUGCCUCCUCGUCGGAGC 1012 ACUCCU 53335_4_460 BCL11a Exon 4 − chr2: 60460849-60460874 AGACAAUCGCCUUUUGCCU 1013 CCUCGU 53335_4_461 BCL11a Exon 4 − chr2: 60460884-60460909 AGCUCAAAGAUCCCUUCCU 1014 UAGCUU 53335_4_462 BCL11a Exon 4 − chr2: 60460913-60460938 GUGGCUCGCCGGCUACGCG 1015 GCCUCC 53335_4_463 BCL11a Exon 4 − chr2: 60460921-60460946 UACUCGCAGUGGCUCGCCG 1016 GCUACG 53335_4_464 BCL11a Exon 4 − chr2: 60460929-60460954 AGAACGUGUACUCGCAGUG 1017 GCUCGC 53335_4_465 BCL11a Exon 4 − chr2: 60460937-60460962 CAACACGGAGAACGUGUAC 1018 UCGCAG 53335_4_466 BCL11a Exon 4 − chr2: 60460957-60460982 CUGCCCCCGGCCGCGAUGC 1019 CCAACA 53335_4_467 BCL11a Exon 4 − chr2: 60460975-60461000 CUCGAGAAGGAGUUCGACC 1020 UGCCCC 53335_4_468 BCL11a Exon 4 − chr2: 60460993-60461018 UUCUCUAAGCGCAUCAAGC 1021 UCGAGA 53335_4_469 BCL11a Exon 4 − chr2: 60461043-60461068 GGGGCCUGUCCAAAAAGCU 1022 GCUGCU 53335_4_470 BCL11a Exon 4 − chr2: 60461044-60461069 GGGGGCCUGUCCAAAAAGC 1023 UGCUGC 53335_4_471 BCL11a Exon 4 − chr2: 60461067-60461092 GCUCCCCGGGCGAGUCGGC 1024 CUCGGG 53335_4_472 BCL11a Exon 4 − chr2: 60461068-60461093 UGCUCCCCGGGCGAGUCGG 1025 CCUCGG 53335_4_473 BCL11a Exon 4 − chr2: 60461069-60461094 CUGCUCCCCGGGCGAGUCG 1026 GCCUCG 53335_4_474 BCL11a Exon 4 − chr2: 60461070-60461095 GCUGCUCCCCGGGCGAGUC 1027 GGCCUC 53335_4_475 BCL11a Exon 4 − chr2: 60461071-60461096 GGCUGCUCCCCGGGCGAGU 1028 CGGCCU 53335_4_476 BCL11a Exon 4 − chr2: 60461077-60461102 GGCCGCGGCUGCUCCCCGG 1029 GCGAGU 53335_4_477 BCL11a Exon 4 − chr2: 60461085-60461110 CUGUUAAUGGCCGCGGCUG 1030 CUCCCC 53335_4_478 BCL11a Exon 4 − chr2: 60461086-60461111 ACUGUUAAUGGCCGCGGCU 1031 GCUCCC 53335_4_479 BCL11a Exon 4 − chr2: 60461097-60461122 UAGACGAUGGCACUGUUAA 1032 UGGCCG 53335_4_480 BCL11a Exon 4 − chr2: 60461103-60461128 ACCGCAUAGACGAUGGCAC 1033 UGUUAA 53335_4_481 BCL11a Exon 4 − chr2: 60461115-60461140 CCGGCGAGUCGGACCGCAU 1034 AGACGA 53335_4_482 BCL11a Exon 4 − chr2: 60461131-60461156 GACGAAGACUCGGUGGCCG 1035 GCGAGU 53335_4_483 BCL11a Exon 4 − chr2: 60461139-60461164 ACACUUGCGACGAAGACUC 1036 GGUGGC 53335_4_484 BCL11a Exon 4 − chr2: 60461143-60461168 AGGGACACUUGCGACGAAG 1037 ACUCGG 53335_4_485 BCL11a Exon 4 − chr2: 60461146-60461171 CACAGGGACACUUGCGACG 1038 AAGACU 53335_4_486 BCL11a Exon 4 − chr2: 60461167-60461192 CACCUGGCCGAGGCCGAGG 1039 GCCACA 53335_4_487 BCL11a Exon 4 − chr2: 60461168-60461193 CCACCUGGCCGAGGCCGAG 1040 GGCCAC 53335_4_488 BCL11a Exon 4 − chr2: 60461175-60461200 AGCGCGGCCACCUGGCCGA 1041 GGCCGA 53335_4_489 BCL11a Exon 4 − chr2: 60461176-60461201 AAGCGCGGCCACCUGGCCG 1042 AGGCCG 53335_4_490 BCL11a Exon 4 − chr2: 60461182-60461207 AAGCAUAAGCGCGGCCACC 1043 UGGCCG 53335_4_491 BCL11a Exon 4 − chr2: 60461188-60461213 GGCGAGAAGCAUAAGCGCG 1044 GCCACC 53335_4_492 BCL11a Exon 4 − chr2: 60461196-60461221 AGGUCCUGGGCGAGAAGCA 1045 UAAGCG 53335_4_493 BCL11a Exon 4 − chr2: 60461214-60461239 UCAGCGAGGCCUUCCACCA 1046 GGUCCU 53335_4_494 BCL11a Exon 4 − chr2: 60461215-60461240 UUCAGCGAGGCCUUCCACC 1047 AGGUCC 53335_4_495 BCL11a Exon 4 − chr2: 60461221-60461246 CAGCACUUCAGCGAGGCCU 1048 UCCACC 53335_4_496 BCL11a Exon 4 − chr2: 60461233-60461258 CUCAGCUCCAUGCAGCACU 1049 UCAGCG 53335_4_497 BCL11a Exon 4 − chr2: 60461263-60461288 GCCCUGCCCGACGUCAUGC 1050 AGGGCA 53335_4_498 BCL11a Exon 4 − chr2: 60461268-60461293 GCCGCGCCCUGCCCGACGU 1051 CAUGCA 53335_4_499 BCL11a Exon 4 − chr2: 60461269-60461294 AGCCGCGCCCUGCCCGACG 1052 UCAUGC 53335_4_500 BCL11a Exon 4 − chr2: 60461304-60461329 GCUCGCGGGGCGCGGUCGU 1053 GGGCGU 53335_4_501 BCL11a Exon 4 − chr2: 60461305-60461330 AGCUCGCGGGGCGCGGUCG 1054 UGGGCG 53335_4_502 BCL11a Exon 4 − chr2: 60461310-60461335 AGAACAGCUCGCGGGGCGC 1055 GGUCGU 53335_4_503 BCL11a Exon 4 − chr2: 60461311-60461336 GAGAACAGCUCGCGGGGCG 1056 CGGUCG 53335_4_504 BCL11a Exon 4 − chr2: 60461317-60461342 CACCACGAGAACAGCUCGC 1057 GGGGCG 53335_4_505 BCL11a Exon 4 − chr2: 60461322-60461347 CGCGCCACCACGAGAACAG 1058 CUCGCG 53335_4_506 BCL11a Exon 4 − chr2: 60461323-60461348 GCGCGCCACCACGAGAACA 1059 GCUCGC 53335_4_507 BCL11a Exon 4 − chr2: 60461324-60461349 GGCGCGCCACCACGAGAAC 1060 AGCUCG 53335_4_508 BCL11a Exon 4 − chr2: 60461350-60461375 UACGGCUUCGGGCUGAGCC 1061 UGGAGG 53335_4_509 BCL11a Exon 4 − chr2: 60461353-60461378 GACUACGGCUUCGGGCUGA 1062 GCCUGG 53335_4_510 BCL11a Exon 4 − chr2: 60461356-60461381 CUGGACUACGGCUUCGGGC 1063 UGAGCC 53335_4_511 BCL11a Exon 4 − chr2: 60461366-60461391 CUCGCUCUCCCUGGACUAC 1064 GGCUUC 53335_4_512 BCL11a Exon 4 − chr2: 60461367-60461392 UCUCGCUCUCCCUGGACUA 1065 CGGCUU 53335_4_513 BCL11a Exon 4 − chr2: 60461373-60461398 ACUGCCUCUCGCUCUCCCU 1066 GGACUA 53335_4_514 BCL11a Exon 4 − chr2: 60461380-60461405 CUCCUCGACUGCCUCUCGC 1067 UCUCCC 53335_4_515 BCL11a Exon 4 − chr2: 60461512-60461537 GCCAGCAGCGCGCUCAAGU 1068 CCGUGG 53335_4_516 BCL11a Exon 4 − chr2: 60461515-60461540 AGCGCCAGCAGCGCGCUCA 1069 AGUCCG 53335_4_517 BCL11a Exon 4 − chr2: 60461544-60461569 CGGAACCCGGCACCAGCGA 1070 CUUGGU 53335_4_518 BCL11a Exon 4 − chr2: 60461545-60461570 CCGGAACCCGGCACCAGCG 1071 ACUUGG 53335_4_519 BCL11a Exon 4 − chr2: 60461548-60461573 UCCCCGGAACCCGGCACCA 1072 GCGACU 53335_4_520 BCL11a Exon 4 − chr2: 60461562-60461587 UCUCCACCGCCAGCUCCCCG 1073 GAACC 53335_4_521 BCL11a Exon 4 − chr2: 60461569-60461594 GACGGUCUCUCCACCGCCA 1074 GCUCCC 53335_4_522 BCL11a Exon 4 − chr2: 60461592-60461617 CCCCCAUGACGGUCAAGUC 1075 CGACGA 53335_4_523 BCL11a Exon 4 − chr2: 60461608-60461633 CACAUGCACAAAUCGUCCC 1076 CCAUGA 53335_4_524 BCL11a Exon 4 − chr2: 60461665-60461690 AACCUGUGCGACCACGCGU 1077 GCACCC 53335_4_525 BCL11a Exon 4 − chr2: 60461712-60461737 UGGUGGUGCACCGGCGCAG 1078 CCACAC 53335_4_526 BCL11a Exon 4 − chr2: 60461713-60461738 CUGGUGGUGCACCGGCGCA 1079 GCCACA 53335_4_527 BCL11a Exon 4 − chr2: 60461726-60461751 AUUUCAGAGCAACCUGGUG 1080 GUGCAC 53335_4_528 BCL11a Exon 4 − chr2: 60461734-60461759 ACGUUCAAAUUUCAGAGCA 1081 ACCUGG 53335_4_529 BCL11a Exon 4 − chr2: 60461737-60461762 AAGACGUUCAAAUUUCAGA 1082 GCAACC 53335_4_530 BCL11a Exon 4 − chr2: 60461766-60461791 UCAAGUCCAAGUCAUGCGA 1083 GUUCUG 53335_4_531 BCL11a Exon 4 − chr2: 60461794-60461819 UCCGCCCCUCCUCCCUCCCA 1084 GCCCC 53335_4_532 BCL11a Exon 4 − chr2: 60461848-60461873 CAGCCAGGUAGCAAGCCGC 1085 CCUUCC 53335_4_533 BCL11a Exon 4 − chr2: 60461868-60461893 AAAGGUUACUGCAACCAUU 1086 CCAGCC 53335_4_534 BCL11a Exon 4 − chr2: 60461891-60461916 CCCAGGCCGGCCCAGCCCU 1087 AUGCAA 53335_4_535 BCL11a Exon 4 − chr2: 60461909-60461934 GUCUAGCCCACCGCUGUCC 1088 CCAGGC 53335_4_536 BCL11a Exon 4 − chr2: 60461913-60461938 ACACGUCUAGCCCACCGCU 1089 GUCCCC 53335_4_537 BCL11a Exon 4 − chr2: 60461942-60461967 CUCUAGGAGACUUAGAGAG 1090 CUGGCA 53335_4_538 BCL11a Exon 4 − chr2: 60461943-60461968 UCUCUAGGAGACUUAGAGA 1091 GCUGGC 53335_4_539 BCL11a Exon 4 − chr2: 60461947-60461972 GAUUUCUCUAGGAGACUUA 1092 GAGAGC 53335_4_540 BCL11a Exon 4 − chr2: 60461963-60461988 GGAGCCUCCCGCCAUGGAU 1093 UUCUCU 53335_4_541 BCL11a Exon 4 − chr2: 60461974-60461999 CCAAUGGCUAUGGAGCCUC 1094 CCGCCA 53335_4_542 BCL11a Exon 4 − chr2: 60461989-60462014 GUGCUGCGGUUGAAUCCAA 1095 UGGCUA 53335_4_543 BCL11a Exon 4 − chr2: 60461995-60462020 GACAGGGUGCUGCGGUUGA 1096 AUCCAA 53335_4_544 BCL11a Exon 4 − chr2: 60462008-60462033 CCCGAGUGCCUUUGACAGG 1097 GUGCUG 53335_4_545 BCL11a Exon 4 − chr2: 60462016-60462041 ACCCAUCACCCGAGUGCCU 1098 UUGACA 53335_4_546 BCL11a Exon 4 − chr2: 60462017-60462042 CACCCAUCACCCGAGUGCC 1099 UUUGAC 53335_4_547 BCL11a Exon 4 − chr2: 60462046-60462071 CGCCUGGGGGCGGAAGAGA 1100 UGGCCC 53335_4_548 BCL11a Exon 4 − chr2: 60462052-60462077 AUAGAGCGCCUGGGGGCGG 1101 AAGAGA 53335_4_549 BCL11a Exon 4 − chr2: 60462061-60462086 CCCCACCGCAUAGAGCGCC 1102 UGGGGG 53335_4_550 BCL11a Exon 4 − chr2: 60462064-60462089 GACCCCCACCGCAUAGAGC 1103 GCCUGG 53335_4_551 BCL11a Exon 4 − chr2: 60462065-60462090 GGACCCCCACCGCAUAGAG 1104 CGCCUG 53335_4_552 BCL11a Exon 4 − chr2: 60462066-60462091 UGGACCCCCACCGCAUAGA 1105 GCGCCU 53335_4_553 BCL11a Exon 4 − chr2: 60462067-60462092 UUGGACCCCCACCGCAUAG 1106 AGCGCC 53335_4_554 BCL11a Exon 4 − chr2: 60462091-60462116 UUUAGUCCACCACCGAGAC 1107 AUCACU 53335_4_555 BCL11a Exon 4 − chr2: 60462143-60462168 GAGAGAGGCUUCCGGCCUG 1108 GCAGAA 53335_4_556 BCL11a Exon 4 − chr2: 60462144-60462169 CGAGAGAGGCUUCCGGCCU 1109 GGCAGA 53335_4_557 BCL11a Exon 4 − chr2: 60462151-60462176 UCAGUAUCGAGAGAGGCUU 1110 CCGGCC 53335_4_558 BCL11a Exon 4 − chr2: 60462156-60462181 CAGGAUCAGUAUCGAGAGA 1111 GGCUUC 53335_4_559 BCL11a Exon 4 − chr2: 60462163-60462188 AGAAUACCAGGAUCAGUAU 1112 CGAGAG 53335_4_560 BCL11a Exon 4 − chr2: 60462180-60462205 ACCCCUUUAACCUGCUAAG 1113 AAUACC 53335_4_561 BCL11a Exon 4 − chr2: 60462227-60462252 AUGUCCUUCCCAGCCACCU 1114 CUCCAU 53335_4_562 BCL11a Exon 4 − chr2: 60462228-60462253 AAUGUCCUUCCCAGCCACC 1115 UCUCCA 53335_4_563 BCL11a Exon 4 − chr2: 60462261-60462286 CGCGGGUUGGUAUCCCUUC 1116 AGGACU 53335_4_564 BCL11a Exon 4 − chr2: 60462267-60462292 UGACCCCGCGGGUUGGUAU 1117 CCCUUC 53335_4_565 BCL11a Exon 4 − chr2: 60462279-60462304 ACGGAAGUCCCCUGACCCC 1118 GCGGGU 53335_4_566 BCL11a Exon 4 − chr2: 60462283-60462308 GAACACGGAAGUCCCCUGA 1119 CCCCGC 53335_4_567 BCL11a Exon 4 − chr2: 60462284-60462309 CGAACACGGAAGUCCCCUG 1120 ACCCCG 53335_4_568 BCL11a Exon 4 − chr2: 60462303-60462328 UAAGAAUCUACUUAGAAAG 1121 CGAACA 53335_4_569 BCL11a Exon 4 − chr2: 60462333-60462358 UCUUGCAACACGCACAGAA 1122 CACUCA 53335_4_570 BCL11a Exon 4 − chr2: 60462365-60462390 UUGCAAACAGCCAUUCACC 1123 AGUGCA 53335_3_1 BCL11a Exon 3 + chr2: 60468716-60468741 UAAGGCUCAACUUACAAAU 1124 ACCCUG 53335_3_2 BCL11a Exon 3 + chr2: 60468717-60468742 AAGGCUCAACUUACAAAUA 1125 CCCUGC 53335_3_3 BCL11a Exon 3 + chr2: 60468718-60468743 AGGCUCAACUUACAAAUAC 1126 CCUGCG 53335_3_4 BCL11a Exon 3 + chr2: 60468740-60468765 GCGGGGCAUAUUCUGCACU 1127 CAUCCC 53335_3_5 BCL11a Exon 3 + chr2: 60468745-60468770 GCAUAUUCUGCACUCAUCC 1128 CAGGCG 53335_3_6 BCL11a Exon 3 + chr2: 60468746-60468771 CAUAUUCUGCACUCAUCCC 1129 AGGCGU 53335_3_7 BCL11a Exon 3 + chr2: 60468747-60468772 AUAUUCUGCACUCAUCCCA 1130 GGCGUG 53335_3_8 BCL11a Exon 3 + chr2: 60468773-60468798 GGAUUAGAGCUCCAUGUGC 1131 AGAACG 53335_3_9 BCL11a Exon 3 + chr2: 60468774-60468799 GAUUAGAGCUCCAUGUGCA 1132 GAACGA 53335_3_10 BCL11a Exon 3 + chr2: 60468775-60468800 AUUAGAGCUCCAUGUGCAG 1133 AACGAG 53335_3_11 BCL11a Exon 3 + chr2: 60468778-60468803 AGAGCUCCAUGUGCAGAAC 1134 GAGGGG 53335_3_12 BCL11a Exon 3 + chr2: 60468783-60468808 UCCAUGUGCAGAACGAGGG 1135 GAGGAG 53335_3_13 BCL11a Exon 3 − chr2: 60468739-60468764 GGAUGAGUGCAGAAUAUGC 1136 CCCGCA 53335_3_14 BCL11a Exon 3 − chr2: 60468740-60468765 GGGAUGAGUGCAGAAUAUG 1137 CCCCGC 53335_3_15 BCL11a Exon 3 − chr2: 60468765-60468790 ACAUGGAGCUCUAAUCCCC 1138 ACGCCU 53335_3_16 BCL11a Exon 3 − chr2: 60468766-60468791 CACAUGGAGCUCUAAUCCC 1139 CACGCC 53335_3_17 BCL11a Exon 3 − chr2: 60468787-60468812 GCCUCUCCUCCCCUCGUUC 1140 UGCACA 53335_3_18 BCL11a Exon 3 − chr2: 60468814-60468839 UCACAGAUAAACUUCUGCA 1141 CUGGAG 53335_3_19 BCL11a Exon 3 − chr2: 60468815-60468840 UUCACAGAUAAACUUCUGC 1142 ACUGGA 53335_3_20 BCL11a Exon 3 − chr2: 60468816-60468841 UUUCACAGAUAAACUUCUG 1143 CACUGG 53335_3_21 BCL11a Exon 3 − chr2: 60468819-60468844 UUCUUUCACAGAUAAACUU 1144 CUGCAC 53335_2_1 BCL11a Exon 2 + chr2: 60545963-60545988 CAUUUACCUGCUAUGUGUU 1145 CCUGUU 53335_2_2 BCL11a Exon 2 + chr2: 60545964-60545989 AUUUACCUGCUAUGUGUUC 1146 CUGUUU 53335_2_3 BCL11a Exon 2 + chr2: 60545965-60545990 UUUACCUGCUAUGUGUUCC 1147 UGUUUG 53335_2_4 BCL11a Exon 2 + chr2: 60546009-60546034 ACGUUGAUAAACAAUCGUC 1148 AUCCUC 53335_2_5 BCL11a Exon 2 + chr2: 60546019-60546044 ACAAUCGUCAUCCUCUGGC 1149 GUGACC 53335_2_6 BCL11a Exon 2 + chr2: 60546035-60546060 GGCGUGACCUGGAUGCCAA 1150 CCUCCA 53335_2_7 BCL11a Exon 2 + chr2: 60546036-60546061 GCGUGACCUGGAUGCCAAC 1151 CUCCAC 53335_2_8 BCL11a Exon 2 + chr2: 60546041-60546066 ACCUGGAUGCCAACCUCCA 1152 CGGGAU 53335_2_9 BCL11a Exon 2 + chr2: 60546063-60546088 GAUUGGAUGCUUUUUUCAU 1153 CUCGAU 53335_2_10 BCL11a Exon 2 + chr2: 60546069-60546094 AUGCUUUUUUCAUCUCGAU 1154 UGGUGA 53335_2_11 BCL11a Exon 2 + chr2: 60546070-60546095 UGCUUUUUUCAUCUCGAUU 1155 GGUGAA 53335_2_12 BCL11a Exon 2 + chr2: 60546071-60546096 GCUUUUUUCAUCUCGAUUG 1156 GUGAAG 53335_2_13 BCL11a Exon 2 + chr2: 60546075-60546100 UUUUCAUCUCGAUUGGUGA 1157 AGGGGA 53335_2_14 BCL11a Exon 2 + chr2: 60546078-60546103 UCAUCUCGAUUGGUGAAGG 1158 GGAAGG 53335_2_15 BCL11a Exon 2 + chr2: 60546106-60546131 CUUAUCCACAGCUUUUUCU 1159 AAGCAG 53335_2_16 BCL11a Exon 2 + chr2: 60546162-60546187 CGAUAAAAAUAAGAAUGUC 1160 CCCCAA 53335_2_17 BCL11a Exon 2 + chr2: 60546163-60546188 GAUAAAAAUAAGAAUGUCC 1161 CCCAAU 53335_2_18 BCL11a Exon 2 + chr2: 60546175-60546200 AAUGUCCCCCAAUGGGAAG 1162 UUCAUC 53335_2_19 BCL11a Exon 2 + chr2: 60546188-60546213 GGGAAGUUCAUCUGGCACU 1163 GCCCAC 53335_2_20 BCL11a Exon 2 + chr2: 60546193-60546218 GUUCAUCUGGCACUGCCCA 1164 CAGGUG 53335_2_21 BCL11a Exon 2 + chr2: 60546196-60546221 CAUCUGGCACUGCCCACAG 1165 GUGAGG 53335_2_22 BCL11a Exon 2 + chr2: 60546213-60546238 AGGUGAGGAGGUCAUGAUC 1166 CCCUUC 53335_2_23 BCL11a Exon 2 + chr2: 60546225-60546250 CAUGAUCCCCUUCUGGAGC 1167 UCCCAA 53335_2_24 BCL11a Exon 2 + chr2: 60546226-60546251 AUGAUCCCCUUCUGGAGCU 1168 CCCAAC 53335_2_25 BCL11a Exon 2 + chr2: 60546232-60546257 CCCUUCUGGAGCUCCCAAC 1169 GGGCCG 53335_2_26 BCL11a Exon 2 + chr2: 60546237-60546262 CUGGAGCUCCCAACGGGCC 1170 GUGGUC 53335_2_27 BCL11a Exon 2 + chr2: 60546257-60546282 UGGUCUGGUUCAUCAUCUG 1171 UAAGAA 53335_2_28 BCL11a Exon 2 + chr2: 60546267-60546292 CAUCAUCUGUAAGAAUGGC 1172 UUCAAG 53335_2_29 BCL11a Exon 2 + chr2: 60546272-60546297 UCUGUAAGAAUGGCUUCAA 1173 GAGGCU 53335_2_30 BCL11a Exon 2 + chr2: 60546278-60546303 AGAAUGGCUUCAAGAGGCU 1174 CGGCUG 53335_2_31 BCL11a Exon 2 + chr2: 60546282-60546307 UGGCUUCAAGAGGCUCGGC 1175 UGUGGU 53335_2_32 BCL11a Exon 2 − chr2: 60545956-60545981 ACACAUAGCAGGUAAAUGA 1176 GAAGCA 53335_2_33 BCL11a Exon 2 − chr2: 60545972-60545997 UUUGCCCCAAACAGGAACA 1177 CAUAGC 53335_2_34 BCL11a Exon 2 − chr2: 60545985-60546010 UCAUCUAGAGGAAUUUGCC 1178 CCAAAC 53335_2_35 BCL11a Exon 2 − chr2: 60546002-60546027 ACGAUUGUUUAUCAACGUC 1179 AUCUAG 53335_2_36 BCL11a Exon 2 − chr2: 60546033-60546058 GAGGUUGGCAUCCAGGUCA 1180 CGCCAG 53335_2_37 BCL11a Exon 2 − chr2: 60546045-60546070 UCCAAUCCCGUGGAGGUUG 1181 GCAUCC 53335_2_38 BCL11a Exon 2 − chr2: 60546053-60546078 AAAAAGCAUCCAAUCCCGU 1182 GGAGGU 53335_2_39 BCL11a Exon 2 − chr2: 60546057-60546082 AUGAAAAAAGCAUCCAAUC 1183 CCGUGG 53335_2_40 BCL11a Exon 2 − chr2: 60546060-60546085 GAGAUGAAAAAAGCAUCCA 1184 AUCCCG 53335_2_41 BCL11a Exon 2 − chr2: 60546114-60546139 GGCAGCCUCUGCUUAGAAA 1185 AAGCUG 53335_2_42 BCL11a Exon 2 − chr2: 60546140-60546165 UCGAGCACAAACGGAAACA 1186 AUGCAA 53335_2_43 BCL11a Exon 2 − chr2: 60546154-60546179 CAUUCUUAUUUUUAUCGAG 1187 CACAAA 53335_2_44 BCL11a Exon 2 − chr2: 60546183-60546208 CAGUGCCAGAUGAACUUCC 1188 CAUUGG 53335_2_45 BCL11a Exon 2 − chr2: 60546184-60546209 GCAGUGCCAGAUGAACUUC 1189 CCAUUG 53335_2_46 BCL11a Exon 2 − chr2: 60546185-60546210 GGCAGUGCCAGAUGAACUU 1190 CCCAUU 53335_2_47 BCL11a Exon 2 − chr2: 60546186-60546211 GGGCAGUGCCAGAUGAACU 1191 UCCCAU 53335_2_48 BCL11a Exon 2 − chr2: 60546211-60546236 AGGGGAUCAUGACCUCCUC 1192 ACCUGU 53335_2_49 BCL11a Exon 2 − chr2: 60546212-60546237 AAGGGGAUCAUGACCUCCU 1193 CACCUG 53335_2_50 BCL11a Exon 2 − chr2: 60546234-60546259 CACGGCCCGUUGGGAGCUC 1194 CAGAAG 53335_2_51 BCL11a Exon 2 − chr2: 60546235-60546260 CCACGGCCCGUUGGGAGCU 1195 CCAGAA 53335_2_52 BCL11a Exon 2 − chr2: 60546236-60546261 ACCACGGCCCGUUGGGAGC 1196 UCCAGA 53335_2_53 BCL11a Exon 2 − chr2: 60546248-60546273 AUGAUGAACCAGACCACGG 1197 CCCGUU 53335_2_54 BCL11a Exon 2 − chr2: 60546249-60546274 GAUGAUGAACCAGACCACG 1198 GCCCGU 53335_2_55 BCL11a Exon 2 − chr2: 60546257-60546282 UUCUUACAGAUGAUGAACC 1199 AGACCA 53335_1_1 BCL11a Exon 1 + chr2: 60553216-60553241 CGAGAAUUCCCGUUUGCUU 1200 AAGUGC 53335_1_2 BCL11a Exon 1 + chr2: 60553217-60553242 GAGAAUUCCCGUUUGCUUA 1201 AGUGCU 53335_1_3 BCL11a Exon 1 + chr2: 60553218-60553243 AGAAUUCCCGUUUGCUUAA 1202 GUGCUG 53335_1_4 BCL11a Exon 1 + chr2: 60553234-60553259 UAAGUGCUGGGGUUUGCCU 1203 UGCUUG 53335_1_5 BCL11a Exon 1 + chr2: 60553244-60553269 GGUUUGCCUUGCUUGCGGC 1204 GAGACA 53335_1_6 BCL11a Exon 1 + chr2: 60553247-60553272 UUGCCUUGCUUGCGGCGAG 1205 ACAUGG 53335_1_7 BCL11a Exon 1 + chr2: 60553248-60553273 UGCCUUGCUUGCGGCGAGA 1206 CAUGGU 53335_1_8 BCL11a Exon 1 + chr2: 60553254-60553279 GCUUGCGGCGAGACAUGGU 1207 GGGCUG 53335_1_9 BCL11a Exon 1 + chr2: 60553255-60553280 CUUGCGGCGAGACAUGGUG 1208 GGCUGC 53335_1_10 BCL11a Exon 1 + chr2: 60553256-60553281 UUGCGGCGAGACAUGGUGG 1209 GCUGCG 53335_1_11 BCL11a Exon 1 + chr2: 60553291-60553316 CGGCGGCGGCGGCGGCGGC 1210 GGCGGG 53335_1_12 BCL11a Exon 1 + chr2: 60553298-60553323 GGCGGCGGCGGCGGCGGGC 1211 GGACGA 53335_1_13 BCL11a Exon 1 + chr2: 60553303-60553328 CGGCGGCGGCGGGCGGACG 1212 ACGGCU 53335_1_14 BCL11a Exon 1 + chr2: 60553313-60553338 GGGCGGACGACGGCUCGGU 1213 UCACAU 53335_1_15 BCL11a Exon 1 + chr2: 60553314-60553339 GGCGGACGACGGCUCGGUU 1214 CACAUC 53335_1_16 BCL11a Exon 1 + chr2: 60553322-60553347 ACGGCUCGGUUCACAUCGG 1215 GAGAGC 53335_1_17 BCL11a Exon 1 + chr2: 60553323-60553348 CGGCUCGGUUCACAUCGGG 1216 AGAGCC 53335_1_18 BCL11a Exon 1 + chr2: 60553335-60553360 CAUCGGGAGAGCCGGGUUA 1217 GAAAGA 53335_1_19 BCL11a Exon 1 + chr2: 60553406-60553431 AAAUAAAUUAGAAAUAAUA 1218 CAAAGA 53335_1_20 BCL11a Exon 1 + chr2: 60553412-60553437 AUUAGAAAUAAUACAAAGA 1219 UGGCGC 53335_1_21 BCL11a Exon 1 + chr2: 60553413-60553438 UUAGAAAUAAUACAAAGAU 1220 GGCGCA 53335_1_22 BCL11a Exon 1 + chr2: 60553427-60553452 AAGAUGGCGCAGGGAAGAU 1221 GAAUUG 53335_1_23 BCL11a Exon 1 + chr2: 60553428-60553453 AGAUGGCGCAGGGAAGAUG 1222 AAUUGU 53335_1_24 BCL11a Exon 1 + chr2: 60553441-60553466 AAGAUGAAUUGUGGGAGAG 1223 CCGUCA 53335_1_25 BCL11a Exon 1 − chr2: 60553227-60553252 GGCAAACCCCAGCACUUAA 1224 GCAAAC 53335_1_26 BCL11a Exon 1 − chr2: 60553228-60553253 AGGCAAACCCCAGCACUUA 1225 AGCAAA 53335_1_27 BCL11a Exon 1 − chr2: 60553253-60553278 AGCCCACCAUGUCUCGCCG 1226 CAAGCA 53335_1_28 BCL11a Exon 1 − chr2: 60553349-60553374 CUCUGGAGUCUCCUUCUUU 1227 CUAACC 53335_1_29 BCL11a Exon 1 − chr2: 60553371-60553396 AAGGCACUGAUGAAGAUAU 1228 UUUCUC 53335_1_30 BCL11a Exon 1 − chr2: 60553395-60553420 UUUCUAAUUUAUUUUGGAU 1229 GUCAAA 53335_1_31 BCL11a Exon 1 − chr2: 60553406-60553431 UCUUUGUAUUAUUUCUAAU 1230 UUAUUU 53335_1_32 BCL11a Exon 1 − chr2: 60553463-60553488 AAAAAAGCUUAAAAAAAAG 1231 CCAUGA

TABLE 2 gRNA targeting domains targeting BCL11a Intron 2 (e.g., to a BCL11a Enhancer) SEQ Target Targeting Site ID Id. Target Region Strand (hg38) gRNA Targeting Domain NO: 53335_I2_1 BCL11a Intron 2 + chr2: 60494277-60494302 GGGAGUUUGGCUUCUCA 1232 UCUGUGCA 53335_I2_2 BCL11a Intron 2 + chr2: 60494289-60494314 UCUCAUCUGUGCAUGGC 1233 CUCUAAAC 53335_I2_3 BCL11a Intron 2 + chr2: 60494290-60494315 CUCAUCUGUGCAUGGCC 1234 UCUAAACU 53335_I2_4 BCL11a Intron 2 + chr2: 60494302-60494327 UGGCCUCUAAACUGGGC 1235 AGUGACCA 53335_I2_5 BCL11a Intron 2 + chr2: 60494307-60494332 UCUAAACUGGGCAGUGA 1236 CCAUGGCC 53335_I2_6 BCL11a Intron 2 + chr2: 60494324-60494349 CCAUGGCCUGGUCACCU 1237 CCCCACUC 53335_I2_7 BCL11a Intron 2 + chr2: 60494330-60494355 CCUGGUCACCUCCCCACU 1238 CUGGACC 53335_I2_8 BCL11a Intron 2 + chr2: 60494331-60494356 CUGGUCACCUCCCCACUC 1239 UGGACCU 53335_I2_9 BCL11a Intron 2 + chr2: 60494351-60494376 GACCUGGGUUGCCCCUC 1240 UGUAAACA 53335_I2_10 BCL11a Intron 2 + chr2: 60494354-60494379 CUGGGUUGCCCCUCUGU 1241 AAACAAGG 53335_I2_11 BCL11a Intron 2 + chr2: 60494418-60494443 AAAUCUUAUGCAAUUUU 1242 UGCCAAGA 53335_I2_12 BCL11a Intron 2 + chr2: 60494419-60494444 AAUCUUAUGCAAUUUUU 1243 GCCAAGAU 53335_I2_13 BCL11a Intron 2 + chr2: 60494426-60494451 UGCAAUUUUUGCCAAGA 1244 UGGGAGUA 53335_I2_14 BCL11a Intron 2 + chr2: 60494427-60494452 GCAAUUUUUGCCAAGAU 1245 GGGAGUAU 53335_I2_15 BCL11a Intron 2 + chr2: 60494428-60494453 CAAUUUUUGCCAAGAUG 1246 GGAGUAUG 53335_I2_16 BCL11a Intron 2 + chr2: 60494440-60494465 AGAUGGGAGUAUGGGGA 1247 GAGAAGAG 53335_I2_17 BCL11a Intron 2 + chr2: 60494446-60494471 GAGUAUGGGGAGAGAAG 1248 AGUGGAAA 53335_I2_18 BCL11a Intron 2 + chr2: 60494477-60494502 AGAGCUCAGUGAGAUGA 1249 GAUAUCAA 53335_I2_19 BCL11a Intron 2 + chr2: 60494478-60494503 GAGCUCAGUGAGAUGAG 1250 AUAUCAAA 53335_I2_20 BCL11a Intron 2 + chr2: 60494479-60494504 AGCUCAGUGAGAUGAGA 1251 UAUCAAAG 53335_I2_21 BCL11a Intron 2 + chr2: 60494518-60494543 UCAUUCCAUCUCCCUAA 1252 UCUCCAAU 53335_I2_22 BCL11a Intron 2 + chr2: 60494533-60494558 AAUCUCCAAUUGGCAAA 1253 GCCAGACU 53335_I2_23 BCL11a Intron 2 + chr2: 60494534-60494559 AUCUCCAAUUGGCAAAG 1254 CCAGACUU 53335_I2_24 BCL11a Intron 2 + chr2: 60494535-60494560 UCUCCAAUUGGCAAAGC 1255 CAGACUUG 53335_I2_25 BCL11a Intron 2 + chr2: 60494548-60494573 AAGCCAGACUUGGGGCA 1256 AUACAGAC 53335_I2_26 BCL11a Intron 2 + chr2: 60494617-60494642 UAUCACCAAAUGUUCUU 1257 UCUUCAGC 53335_I2_27 BCL11a Intron 2 + chr2: 60494631-60494656 CUUUCUUCAGCUGGAAU 1258 UUAAAAUA 53335_I2_28 BCL11a Intron 2 + chr2: 60494649-60494674 UAAAAUAUGGACUCAUC 1259 CGUAAAAU 53335_I2_29 BCL11a Intron 2 + chr2: 60494675-60494700 GGAAUAAUAAUAGUAUA 1260 UGCUUCAU 53335_I2_30 BCL11a Intron 2 + chr2: 60494676-60494701 GAAUAAUAAUAGUAUAU 1261 GCUUCAUA 53335_I2_31 BCL11a Intron 2 + chr2: 60494766-60494791 GCUUGUGAACUAAAAUG 1262 CUGCCUCC 53335_I2_32 BCL11a Intron 2 + chr2: 60494806-60494831 ACACCUCAGCAGAAACA 1263 AAGUUAUC 53335_I2_33 BCL11a Intron 2 + chr2: 60494830-60494855 CAGGCCCUUUCCCCAAU 1264 UCCUAGUU 53335_I2_34 BCL11a Intron 2 + chr2: 60494831-60494856 AGGCCCUUUCCCCAAUU 1265 CCUAGUUU 53335_I2_35 BCL11a Intron 2 + chr2: 60494844-60494869 AAUUCCUAGUUUGGGUC 1266 AGAAGAAA 53335_I2_36 BCL11a Intron 2 + chr2: 60494845-60494870 AUUCCUAGUUUGGGUCA 1267 GAAGAAAA 53335_I2_37 BCL11a Intron 2 + chr2: 60494851-60494876 AGUUUGGGUCAGAAGAA 1268 AAGGGAAA 53335_I2_38 BCL11a Intron 2 + chr2: 60494852-60494877 GUUUGGGUCAGAAGAAA 1269 AGGGAAAA 53335_I2_39 BCL11a Intron 2 + chr2: 60494857-60494882 GGUCAGAAGAAAAGGGA 1270 AAAGGGAG 53335_I2_40 BCL11a Intron 2 + chr2: 60494864-60494889 AGAAAAGGGAAAAGGGA 1271 GAGGAAAA 53335_I2_41 BCL11a Intron 2 + chr2: 60494883-60494908 GGAAAAAGGAAAAGAAU 1272 AUGACGUC 53335_I2_42 BCL11a Intron 2 + chr2: 60494884-60494909 GAAAAAGGAAAAGAAUA 1273 UGACGUCA 53335_I2_43 BCL11a Intron 2 + chr2: 60494885-60494910 AAAAAGGAAAAGAAUAU 1274 GACGUCAG 53335_I2_44 BCL11a Intron 2 + chr2: 60494886-60494911 AAAAGGAAAAGAAUAUG 1275 ACGUCAGG 53335_I2_45 BCL11a Intron 2 + chr2: 60494889-60494914 AGGAAAAGAAUAUGACG 1276 UCAGGGGG 53335_I2_46 BCL11a Intron 2 + chr2: 60494901-60494926 UGACGUCAGGGGGAGGC 1277 AAGUCAGU 53335_I2_47 BCL11a Intron 2 + chr2: 60494902-60494927 GACGUCAGGGGGAGGCA 1278 AGUCAGUU 53335_I2_48 BCL11a Intron 2 + chr2: 60494928-60494953 GGAACACAGAUCCUAAC 1279 ACAGUAGC 53335_I2_49 BCL11a Intron 2 + chr2: 60494939-60494964 CCUAACACAGUAGCUGG 1280 UACCUGAU 53335_I2_50 BCL11a Intron 2 + chr2: 60494955-60494980 GUACCUGAUAGGUGCCU 1281 AUAUGUGA 53335_I2_51 BCL11a Intron 2 + chr2: 60494959-60494984 CUGAUAGGUGCCUAUAU 1282 GUGAUGGA 53335_I2_52 BCL11a Intron 2 + chr2: 60494960-60494985 UGAUAGGUGCCUAUAUG 1283 UGAUGGAU 53335_I2_53 BCL11a Intron 2 + chr2: 60494963-60494988 UAGGUGCCUAUAUGUGA 1284 UGGAUGGG 53335_I2_54 BCL11a Intron 2 + chr2: 60494986-60495011 GGUGGACAGCCCGACAG 1285 AUGAAAAA 53335_I2_55 BCL11a Intron 2 + chr2: 60494998-60495023 GACAGAUGAAAAAUGGA 1286 CAAUUAUG 53335_I2_56 BCL11a Intron 2 + chr2: 60495001-60495026 AGAUGAAAAAUGGACAA 1287 UUAUGAGG 53335_I2_57 BCL11a Intron 2 + chr2: 60495002-60495027 GAUGAAAAAUGGACAAU 1288 UAUGAGGA 53335_I2_58 BCL11a Intron 2 + chr2: 60495003-60495028 AUGAAAAAUGGACAAUU 1289 AUGAGGAG 53335_I2_59 BCL11a Intron 2 + chr2: 60495017-60495042 AUUAUGAGGAGGGGAGA 1290 GUGCAGAC 53335_I2_60 BCL11a Intron 2 + chr2: 60495018-60495043 UUAUGAGGAGGGGAGAG 1291 UGCAGACA 53335_I2_61 BCL11a Intron 2 + chr2: 60495019-60495044 UAUGAGGAGGGGAGAGU 1292 GCAGACAG 53335_I2_62 BCL11a Intron 2 + chr2: 60495045-60495070 GGAAGCUUCACCUCCUU 1293 UACAAUUU 53335_I2_63 BCL11a Intron 2 + chr2: 60495046-60495071 GAAGCUUCACCUCCUUU 1294 ACAAUUUU 53335_I2_64 BCL11a Intron 2 + chr2: 60495057-60495082 UCCUUUACAAUUUUGGG 1295 AGUCCACA 53335_I2_65 BCL11a Intron 2 + chr2: 60495062-60495087 UACAAUUUUGGGAGUCC 1296 ACACGGCA 53335_I2_66 BCL11a Intron 2 + chr2: 60495135-60495160 CAUCACCAAGAGAGCCU 1297 UCCGAAAG 53335_I2_67 BCL11a Intron 2 + chr2: 60495144-60495169 GAGAGCCUUCCGAAAGA 1298 GGCCCCCC 53335_I2_68 BCL11a Intron 2 + chr2: 60495145-60495170 AGAGCCUUCCGAAAGAG 1299 GCCCCCCU 53335_I2_69 BCL11a Intron 2 + chr2: 60495152-60495177 UCCGAAAGAGGCCCCCC 1300 UGGGCAAA 53335_I2_70 BCL11a Intron 2 + chr2: 60495162-60495187 GCCCCCCUGGGCAAACG 1301 GCCACCGA 53335_I2_71 BCL11a Intron 2 + chr2: 60495167-60495192 CCUGGGCAAACGGCCAC 1302 CGAUGGAG 53335_I2_72 BCL11a Intron 2 + chr2: 60495215-60495240 CCACCCACGCCCCCACCC 1303 UAAUCAG 53335_I2_73 BCL11a Intron 2 + chr2: 60495230-60495255 CCCUAAUCAGAGGCCAA 1304 ACCCUUCC 53335_I2_74 BCL11a Intron 2 + chr2: 60495293-60495318 ACUAGCUUCAAAGUUGU 1305 AUUGACCC 53335_I2_75 BCL11a Intron 2 + chr2: 60495333-60495358 AAGAGUAGAUGCCAUAU 1306 CUCUUUUC 53335_I2_76 BCL11a Intron 2 + chr2: 60495354-60495379 UUUCUGGCCUAUGUUAU 1307 UACCUGUA 53335_I2_77 BCL11a Intron 2 + chr2: 60495366-60495391 GUUAUUACCUGUAUGGA 1308 CUUUGCAC 53335_I2_78 BCL11a Intron 2 + chr2: 60495400-60495425 CUAUCUGCUCUUACUUA 1309 UGCACACC 53335_I2_79 BCL11a Intron 2 + chr2: 60495401-60495426 UAUCUGCUCUUACUUAU 1310 GCACACCU 53335_I2_80 BCL11a Intron 2 + chr2: 60495402-60495427 AUCUGCUCUUACUUAUG 1311 CACACCUG 53335_I2_81 BCL11a Intron 2 + chr2: 60495486-60495511 CCUGUCUAGCUGCCUUC 1312 CUUAUCAC 53335_I2_82 BCL11a Intron 2 + chr2: 60495500-60495525 UUCCUUAUCACAGGAAU 1313 AGCACCCA 53335_I2_83 BCL11a Intron 2 + chr2: 60495543-60495568 GAGUAGAACCCCCUAUA 1314 AACUAGUC 53335_I2_84 BCL11a Intron 2 + chr2: 60495554-60495579 CCUAUAAACUAGUCUGG 1315 UUUGCCCA 53335_I2_85 BCL11a Intron 2 + chr2: 60495555-60495580 CUAUAAACUAGUCUGGU 1316 UUGCCCAU 53335_I2_86 BCL11a Intron 2 + chr2: 60495556-60495581 UAUAAACUAGUCUGGUU 1317 UGCCCAUG 53335_I2_87 BCL11a Intron 2 + chr2: 60495566-60495591 UCUGGUUUGCCCAUGGG 1318 GCACAGUC 53335_I2_88 BCL11a Intron 2 + chr2: 60495578-60495603 AUGGGGCACAGUCAGGC 1319 UGUUUUCC 53335_I2_89 BCL11a Intron 2 + chr2: 60495579-60495604 UGGGGCACAGUCAGGCU 1320 GUUUUCCA 53335_I2_90 BCL11a Intron 2 + chr2: 60495582-60495607 GGCACAGUCAGGCUGUU 1321 UUCCAGGG 53335_I2_91 BCL11a Intron 2 + chr2: 60495583-60495608 GCACAGUCAGGCUGUUU 1322 UCCAGGGU 53335_I2_92 BCL11a Intron 2 + chr2: 60495584-60495609 CACAGUCAGGCUGUUUU 1323 CCAGGGUG 53335_I2_93 BCL11a Intron 2 + chr2: 60495661-60495686 ACACACGUAUGUGUUGU 1324 GAUCCCUG 53335_I2_94 BCL11a Intron 2 + chr2: 60495674-60495699 UUGUGAUCCCUGUGGUU 1325 UGAGAGUU 53335_I2_95 BCL11a Intron 2 + chr2: 60495706-60495731 UCCCUAAAAGUCAAAAU 1326 AUUCUCAA 53335_I2_96 BCL11a Intron 2 + chr2: 60495707-60495732 CCCUAAAAGUCAAAAUA 1327 UUCUCAAU 53335_I2_97 BCL11a Intron 2 + chr2: 60495735-60495760 CCCUCAAUCAGCACAUA 1328 CACACAAA 53335_I2_98 BCL11a Intron 2 + chr2: 60495742-60495767 UCAGCACAUACACACAA 1329 AAGGUACC 53335_I2_99 BCL11a Intron 2 + chr2: 60495775-60495800 UGUAAUUCUUUUCCUGC 1330 UCAAAGAC 53335_I2_100 BCL11a Intron 2 + chr2: 60495820-60495845 CCCCAACCAAAAACCCUU 1331 GCCACCA 53335_I2_101 BCL11a Intron 2 + chr2: 60495821-60495846 CCCAACCAAAAACCCUU 1332 GCCACCAU 53335_I2_102 BCL11a Intron 2 + chr2: 60495828-60495853 AAAAACCCUUGCCACCA 1333 UGGGAGCC 53335_I2_103 BCL11a Intron 2 + chr2: 60495829-60495854 AAAACCCUUGCCACCAU 1334 GGGAGCCU 53335_I2_104 BCL11a Intron 2 + chr2: 60495830-60495855 AAACCCUUGCCACCAUG 1335 GGAGCCUG 53335_I2_105 BCL11a Intron 2 + chr2: 60495839-60495864 CCACCAUGGGAGCCUGG 1336 GGCAGAGA 53335_I2_106 BCL11a Intron 2 + chr2: 60495867-60495892 CACAGUGAAGUCAAACU 1337 GUAAUUCC 53335_I2_107 BCL11a Intron 2 + chr2: 60495877-60495902 UCAAACUGUAAUUCCAG 1338 GCUCUAAA 53335_I2_108 BCL11a Intron 2 + chr2: 60495913-60495938 UUUUUCUGAGAGUCUCU 1339 AAAUUACA 53335_I2_109 BCL11a Intron 2 + chr2: 60495914-60495939 UUUUCUGAGAGUCUCUA 1340 AAUUACAA 53335_I2_110 BCL11a Intron 2 + chr2: 60495972-60495997 ACACCUAAGAAACAUAC 1341 UGCAGCUC 53335_I2_111 BCL11a Intron 2 + chr2: 60496001-60496026 AAAGAGAACAAACAAAC 1342 CAAAGAGA 53335_I2_112 BCL11a Intron 2 + chr2: 60496002-60496027 AAGAGAACAAACAAACC 1343 AAAGAGAA 53335_I2_113 BCL11a Intron 2 + chr2: 60496011-60496036 AACAAACCAAAGAGAAG 1344 GGAUCCAG 53335_I2_114 BCL11a Intron 2 + chr2: 60496048-60496073 UAUGUGAAAAGUCAAUU 1345 GAUAAUGA 53335_I2_115 BCL11a Intron 2 + chr2: 60496055-60496080 AAAGUCAAUUGAUAAUG 1346 AAGGCUUU 53335_I2_116 BCL11a Intron 2 + chr2: 60496063-60496088 UUGAUAAUGAAGGCUUU 1347 AGGAUAAC 53335_I2_117 BCL11a Intron 2 + chr2: 60496066-60496091 AUAAUGAAGGCUUUAGG 1348 AUAACCGG 53335_I2_118 BCL11a Intron 2 + chr2: 60496067-60496092 UAAUGAAGGCUUUAGGA 1349 UAACCGGA 53335_I2_119 BCL11a Intron 2 + chr2: 60496068-60496093 AAUGAAGGCUUUAGGAU 1350 AACCGGAG 53335_I2_120 BCL11a Intron 2 + chr2: 60496098-60496123 AUGAUUGAAAGCAAUGC 1351 ACCUGUGC 53335_I2_121 BCL11a Intron 2 + chr2: 60496104-60496129 GAAAGCAAUGCACCUGU 1352 GCAGGAAA 53335_I2_122 BCL11a Intron 2 + chr2: 60496111-60496136 AUGCACCUGUGCAGGAA 1353 AUGGAUUA 53335_I2_123 BCL11a Intron 2 + chr2: 60496118-60496143 UGUGCAGGAAAUGGAUU 1354 ACGGAAAC 53335_I2_124 BCL11a Intron 2 + chr2: 60496119-60496144 GUGCAGGAAAUGGAUUA 1355 CGGAAACA 53335_I2_125 BCL11a Intron 2 + chr2: 60496153-60496178 UCAUGAAAUCCCAGAAA 1356 ACCAGAAC 53335_I2_126 BCL11a Intron 2 + chr2: 60496154-60496179 CAUGAAAUCCCAGAAAA 1357 CCAGAACC 53335_I2_127 BCL11a Intron 2 + chr2: 60496164-60496189 CAGAAAACCAGAACCGG 1358 GAAAGUUC 53335_I2_128 BCL11a Intron 2 + chr2: 60496171-60496196 CCAGAACCGGGAAAGUU 1359 CUGGAAGU 53335_I2_129 BCL11a Intron 2 + chr2: 60496198-60496223 GAAAAACAAAUCAUGAC 1360 UUAAGCAA 53335_I2_130 BCL11a Intron 2 + chr2: 60496238-60496263 CGUUUACAGAAUGCCUU 1361 GUCCCACG 53335_I2_131 BCL11a Intron 2 − chr2: 60494308-60494333 AGGCCAUGGUCACUGCC 1362 CAGUUUAG 53335_I2_132 BCL11a Intron 2 − chr2: 60494327-60494352 CCAGAGUGGGGAGGUGA 1363 CCAGGCCA 53335_I2_133 BCL11a Intron 2 − chr2: 60494333-60494358 CCAGGUCCAGAGUGGGG 1364 AGGUGACC 53335_I2_134 BCL11a Intron 2 − chr2: 60494341-60494366 GGGGCAACCCAGGUCCA 1365 GAGUGGGG 53335_I2_135 BCL11a Intron 2 − chr2: 60494344-60494369 AGAGGGGCAACCCAGGU 1366 CCAGAGUG 53335_I2_136 BCL11a Intron 2 − chr2: 60494345-60494370 CAGAGGGGCAACCCAGG 1367 UCCAGAGU 53335_I2_137 BCL11a Intron 2 − chr2: 60494346-60494371 ACAGAGGGGCAACCCAG 1368 GUCCAGAG 53335_I2_138 BCL11a Intron 2 − chr2: 60494356-60494381 CUCCUUGUUUACAGAGG 1369 GGCAACCC 53335_I2_139 BCL11a Intron 2 − chr2: 60494365-60494390 UAUUACAACCUCCUUGU 1370 UUACAGAG 53335_I2_140 BCL11a Intron 2 − chr2: 60494366-60494391 UUAUUACAACCUCCUUG 1371 UUUACAGA 53335_I2_141 BCL11a Intron 2 − chr2: 60494367-60494392 UUUAUUACAACCUCCUU 1372 GUUUACAG 53335_I2_142 BCL11a Intron 2 − chr2: 60494401-60494426 UAAGAUUUAUAAGACAU 1373 UAGGGUAU 53335_I2_143 BCL11a Intron 2 − chr2: 60494407-60494432 AUUGCAUAAGAUUUAUA 1374 AGACAUUA 53335_I2_144 BCL11a Intron 2 − chr2: 60494408-60494433 AAUUGCAUAAGAUUUAU 1375 AAGACAUU 53335_I2_145 BCL11a Intron 2 − chr2: 60494440-60494465 CUCUUCUCUCCCCAUACU 1376 CCCAUCU 53335_I2_146 BCL11a Intron 2 − chr2: 60494477-60494502 UUGAUAUCUCAUCUCAC 1377 UGAGCUCU 53335_I2_147 BCL11a Intron 2 − chr2: 60494478-60494503 UUUGAUAUCUCAUCUCA 1378 CUGAGCUC 53335_I2_148 BCL11a Intron 2 − chr2: 60494526-60494551 CUUUGCCAAUUGGAGAU 1379 UAGGGAGA 53335_I2_149 BCL11a Intron 2 − chr2: 60494532-60494557 GUCUGGCUUUGCCAAUU 1380 GGAGAUUA 53335_I2_150 BCL11a Intron 2 − chr2: 60494533-60494558 AGUCUGGCUUUGCCAAU 1381 UGGAGAUU 53335_I2_151 BCL11a Intron 2 − chr2: 60494541-60494566 UUGCCCCAAGUCUGGCU 1382 UUGCCAAU 53335_I2_152 BCL11a Intron 2 − chr2: 60494554-60494579 GAACCAGUCUGUAUUGC 1383 CCCAAGUC 53335_I2_153 BCL11a Intron 2 − chr2: 60494599-60494624 GGUGAUAAAUCAUUAGG 1384 AAUGAGCU 53335_I2_154 BCL11a Intron 2 − chr2: 60494610-60494635 AAAGAACAUUUGGUGAU 1385 AAAUCAUU 53335_I2_155 BCL11a Intron 2 − chr2: 60494625-60494650 AAAUUCCAGCUGAAGAA 1386 AGAACAUU 53335_I2_156 BCL11a Intron 2 − chr2: 60494668-60494693 AUAUACUAUUAUUAUUC 1387 CUAUUUUA 53335_I2_157 BCL11a Intron 2 − chr2: 60494745-60494770 AAGCUCGGAGCACUUAC 1388 UCUGCUCU 53335_I2_158 BCL11a Intron 2 − chr2: 60494765-60494790 GAGGCAGCAUUUUAGUU 1389 CACAAGCU 53335_I2_159 BCL11a Intron 2 − chr2: 60494789-60494814 UGAGGUGUAACUAAUAA 1390 AUACCAGG 53335_I2_160 BCL11a Intron 2 − chr2: 60494792-60494817 UGCUGAGGUGUAACUAA 1391 UAAAUACC 53335_I2_161 BCL11a Intron 2 − chr2: 60494812-60494837 GGGCCUGAUAACUUUGU 1392 UUCUGCUG 53335_I2_162 BCL11a Intron 2 − chr2: 60494837-60494862 UGACCCAAACUAGGAAU 1393 UGGGGAAA 53335_I2_163 BCL11a Intron 2 − chr2: 60494838-60494863 CUGACCCAAACUAGGAA 1394 UUGGGGAA 53335_I2_164 BCL11a Intron 2 − chr2: 60494843-60494868 UUCUUCUGACCCAAACU 1395 AGGAAUUG 53335_I2_165 BCL11a Intron 2 − chr2: 60494844-60494869 UUUCUUCUGACCCAAAC 1396 UAGGAAUU 53335_I2_166 BCL11a Intron 2 − chr2: 60494845-60494870 UUUUCUUCUGACCCAAA 1397 CUAGGAAU 53335_I2_167 BCL11a Intron 2 − chr2: 60494851-60494876 UUUCCCUUUUCUUCUGA 1398 CCCAAACU 53335_I2_168 BCL11a Intron 2 − chr2: 60494942-60494967 CCUAUCAGGUACCAGCU 1399 ACUGUGUU 53335_I2_169 BCL11a Intron 2 − chr2: 60494961-60494986 CAUCCAUCACAUAUAGG 1400 CACCUAUC 53335_I2_170 BCL11a Intron 2 − chr2: 60494972-60494997 GGCUGUCCACCCAUCCA 1401 UCACAUAU 53335_I2_171 BCL11a Intron 2 − chr2: 60494998-60495023 CAUAAUUGUCCAUUUUU 1402 CAUCUGUC 53335_I2_172 BCL11a Intron 2 − chr2: 60494999-60495024 UCAUAAUUGUCCAUUUU 1403 UCAUCUGU 53335_I2_173 BCL11a Intron 2 − chr2: 60495058-60495083 GUGUGGACUCCCAAAAU 1404 UGUAAAGG 53335_I2_174 BCL11a Intron 2 − chr2: 60495061-60495086 GCCGUGUGGACUCCCAA 1405 AAUUGUAA 53335_I2_175 BCL11a Intron 2 − chr2: 60495080-60495105 GAAAUAAUUUGUAUGCC 1406 AUGCCGUG 53335_I2_176 BCL11a Intron 2 − chr2: 60495111-60495136 GGAGAAUUGGAUUUUAU 1407 UUCUCAAU 53335_I2_177 BCL11a Intron 2 − chr2: 60495112-60495137 UGGAGAAUUGGAUUUUA 1408 UUUCUCAA 53335_I2_178 BCL11a Intron 2 − chr2: 60495129-60495154 GAAGGCUCUCUUGGUGA 1409 UGGAGAAU 53335_I2_179 BCL11a Intron 2 − chr2: 60495137-60495162 CUCUUUCGGAAGGCUCU 1410 CUUGGUGA 53335_I2_180 BCL11a Intron 2 − chr2: 60495143-60495168 GGGGGCCUCUUUCGGAA 1411 GGCUCUCU 53335_I2_181 BCL11a Intron 2 − chr2: 60495152-60495177 UUUGCCCAGGGGGGCCU 1412 CUUUCGGA 53335_I2_182 BCL11a Intron 2 − chr2: 60495156-60495181 GCCGUUUGCCCAGGGGG 1413 GCCUCUUU 53335_I2_183 BCL11a Intron 2 − chr2: 60495166-60495191 UCCAUCGGUGGCCGUUU 1414 GCCCAGGG 53335_I2_184 BCL11a Intron 2 − chr2: 60495167-60495192 CUCCAUCGGUGGCCGUU 1415 UGCCCAGG 53335_I2_185 BCL11a Intron 2 − chr2: 60495168-60495193 UCUCCAUCGGUGGCCGU 1416 UUGCCCAG 53335_I2_186 BCL11a Intron 2 − chr2: 60495169-60495194 CUCUCCAUCGGUGGCCG 1417 UUUGCCCA 53335_I2_187 BCL11a Intron 2 − chr2: 60495170-60495195 CCUCUCCAUCGGUGGCC 1418 GUUUGCCC 53335_I2_188 BCL11a Intron 2 − chr2: 60495183-60495208 GAGGACUGGCAGACCUC 1419 UCCAUCGG 53335_I2_189 BCL11a Intron 2 − chr2: 60495186-60495211 GAAGAGGACUGGCAGAC 1420 CUCUCCAU 53335_I2_190 BCL11a Intron 2 − chr2: 60495202-60495227 GGGCGUGGGUGGGGUAG 1421 AAGAGGAC 53335_I2_191 BCL11a Intron 2 − chr2: 60495207-60495232 GGUGGGGGCGUGGGUGG 1422 GGUAGAAG 53335_I2_192 BCL11a Intron 2 − chr2: 60495216-60495241 UCUGAUUAGGGUGGGGG 1423 CGUGGGUG 53335_I2_193 BCL11a Intron 2 − chr2: 60495217-60495242 CUCUGAUUAGGGUGGGG 1424 GCGUGGGU 53335_I2_194 BCL11a Intron 2 − chr2: 60495218-60495243 CCUCUGAUUAGGGUGGG 1425 GGCGUGGG 53335_I2_195 BCL11a Intron 2 − chr2: 60495221-60495246 UGGCCUCUGAUUAGGGU 1426 GGGGGCGU 53335_I2_196 BCL11a Intron 2 − chr2: 60495222-60495247 UUGGCCUCUGAUUAGGG 1427 UGGGGGCG 53335_I2_197 BCL11a Intron 2 − chr2: 60495227-60495252 AGGGUUUGGCCUCUGAU 1428 UAGGGUGG 53335_I2_198 BCL11a Intron 2 − chr2: 60495228-60495253 AAGGGUUUGGCCUCUGA 1429 UUAGGGUG 53335_I2_199 BCL11a Intron 2 − chr2: 60495229-60495254 GAAGGGUUUGGCCUCUG 1430 AUUAGGGU 53335_I2_200 BCL11a Intron 2 − chr2: 60495230-60495255 GGAAGGGUUUGGCCUCU 1431 GAUUAGGG 53335_I2_201 BCL11a Intron 2 − chr2: 60495233-60495258 CCAGGAAGGGUUUGGCC 1432 UCUGAUUA 53335_I2_202 BCL11a Intron 2 − chr2: 60495234-60495259 UCCAGGAAGGGUUUGGC 1433 CUCUGAUU 53335_I2_203 BCL11a Intron 2 − chr2: 60495246-60495271 UUUAUCACAGGCUCCAG 1434 GAAGGGUU 53335_I2_204 BCL11a Intron 2 − chr2: 60495251-60495276 UUGCUUUUAUCACAGGC 1435 UCCAGGAA 53335_I2_205 BCL11a Intron 2 − chr2: 60495252-60495277 GUUGCUUUUAUCACAGG 1436 CUCCAGGA 53335_I2_206 BCL11a Intron 2 − chr2: 60495256-60495281 AACAGUUGCUUUUAUCA 1437 CAGGCUCC 53335_I2_207 BCL11a Intron 2 − chr2: 60495263-60495288 GCAAGCUAACAGUUGCU 1438 UUUAUCAC 53335_I2_208 BCL11a Intron 2 − chr2: 60495318-60495343 AUCUACUCUUAGACAUA 1439 ACACACCA 53335_I2_209 BCL11a Intron 2 − chr2: 60495319-60495344 CAUCUACUCUUAGACAU 1440 AACACACC 53335_I2_210 BCL11a Intron 2 − chr2: 60495347-60495372 AAUAACAUAGGCCAGAA 1441 AAGAGAUA 53335_I2_211 BCL11a Intron 2 − chr2: 60495364-60495389 GCAAAGUCCAUACAGGU 1442 AAUAACAU 53335_I2_212 BCL11a Intron 2 − chr2: 60495376-60495401 GCUGAUUCCAGUGCAAA 1443 GUCCAUAC 53335_I2_213 BCL11a Intron 2 − chr2: 60495426-60495451 CGAUACAGGGCUGGCUC 1444 UAUGCCCC 53335_I2_214 BCL11a Intron 2 − chr2: 60495440-60495465 AGAUGGCUGAAAAGCGA 1445 UACAGGGC 53335_I2_215 BCL11a Intron 2 − chr2: 60495444-60495469 AGUGAGAUGGCUGAAAA 1446 GCGAUACA 53335_I2_216 BCL11a Intron 2 − chr2: 60495445-60495470 UAGUGAGAUGGCUGAAA 1447 AGCGAUAC 53335_I2_217 BCL11a Intron 2 − chr2: 60495462-60495487 GACUUGGGAGUUAUCUG 1448 UAGUGAGA 53335_I2_218 BCL11a Intron 2 − chr2: 60495482-60495507 UAAGGAAGGCAGCUAGA 1449 CAGGACUU 53335_I2_219 BCL11a Intron 2 − chr2: 60495483-60495508 AUAAGGAAGGCAGCUAG 1450 ACAGGACU 53335_I2_220 BCL11a Intron 2 − chr2: 60495489-60495514 CCUGUGAUAAGGAAGGC 1451 AGCUAGAC 53335_I2_221 BCL11a Intron 2 − chr2: 60495501-60495526 UUGGGUGCUAUUCCUGU 1452 GAUAAGGA 53335_I2_222 BCL11a Intron 2 − chr2: 60495505-60495530 GACCUUGGGUGCUAUUC 1453 CUGUGAUA 53335_I2_223 BCL11a Intron 2 − chr2: 60495524-60495549 CUACUCUGAGGUACUGA 1454 UGGACCUU 53335_I2_224 BCL11a Intron 2 − chr2: 60495525-60495550 UCUACUCUGAGGUACUG 1455 AUGGACCU 53335_I2_225 BCL11a Intron 2 − chr2: 60495532-60495557 AGGGGGUUCUACUCUGA 1456 GGUACUGA 53335_I2_226 BCL11a Intron 2 − chr2: 60495541-60495566 CUAGUUUAUAGGGGGUU 1457 CUACUCUG 53335_I2_227 BCL11a Intron 2 − chr2: 60495554-60495579 UGGGCAAACCAGACUAG 1458 UUUAUAGG 53335_I2_228 BCL11a Intron 2 − chr2: 60495555-60495580 AUGGGCAAACCAGACUA 1459 GUUUAUAG 53335_I2_229 BCL11a Intron 2 − chr2: 60495556-60495581 CAUGGGCAAACCAGACU 1460 AGUUUAUA 53335_I2_230 BCL11a Intron 2 − chr2: 60495557-60495582 CCAUGGGCAAACCAGAC 1461 UAGUUUAU 53335_I2_231 BCL11a Intron 2 − chr2: 60495578-60495603 GGAAAACAGCCUGACUG 1462 UGCCCCAU 53335_I2_232 BCL11a Intron 2 − chr2: 60495579-60495604 UGGAAAACAGCCUGACU 1463 GUGCCCCA 53335_I2_233 BCL11a Intron 2 − chr2: 60495604-60495629 GGCAGAGAAUGUCUGCA 1464 CCCCACCC 53335_I2_234 BCL11a Intron 2 − chr2: 60495630-60495655 UGACGUUAUAUGUAAGC 1465 AUCACAAC 53335_I2_235 BCL11a Intron 2 − chr2: 60495684-60495709 GGAAGCUCCAAACUCUC 1466 AAACCACA 53335_I2_236 BCL11a Intron 2 − chr2: 60495685-60495710 GGGAAGCUCCAAACUCU 1467 CAAACCAC 53335_I2_237 BCL11a Intron 2 − chr2: 60495710-60495735 CCCAUUGAGAAUAUUUU 1468 GACUUUUA 53335_I2_238 BCL11a Intron 2 − chr2: 60495711-60495736 GCCCAUUGAGAAUAUUU 1469 UGACUUUU 53335_I2_239 BCL11a Intron 2 − chr2: 60495738-60495763 CCUUUUGUGUGUAUGUG 1470 CUGAUUGA 53335_I2_240 BCL11a Intron 2 − chr2: 60495739-60495764 ACCUUUUGUGUGUAUGU 1471 GCUGAUUG 53335_I2_241 BCL11a Intron 2 − chr2: 60495768-60495793 AGCAGGAAAAGAAUUAC 1472 AGUUUUCC 53335_I2_242 BCL11a Intron 2 − chr2: 60495790-60495815 GGUAUUGAAUUGCCUGU 1473 CUUUGAGC 53335_I2_243 BCL11a Intron 2 − chr2: 60495816-60495841 GGCAAGGGUUUUUGGUU 1474 GGGGGAAG 53335_I2_244 BCL11a Intron 2 − chr2: 60495817-60495842 UGGCAAGGGUUUUUGGU 1475 UGGGGGAA 53335_I2_245 BCL11a Intron 2 − chr2: 60495818-60495843 GUGGCAAGGGUUUUUGG 1476 UUGGGGGA 53335_I2_246 BCL11a Intron 2 − chr2: 60495822-60495847 CAUGGUGGCAAGGGUUU 1477 UUGGUUGG 53335_I2_247 BCL11a Intron 2 − chr2: 60495823-60495848 CCAUGGUGGCAAGGGUU 1478 UUUGGUUG 53335_I2_248 BCL11a Intron 2 − chr2: 60495824-60495849 CCCAUGGUGGCAAGGGU 1479 UUUUGGUU 53335_I2_249 BCL11a Intron 2 − chr2: 60495825-60495850 UCCCAUGGUGGCAAGGG 1480 UUUUUGGU 53335_I2_250 BCL11a Intron 2 − chr2: 60495829-60495854 AGGCUCCCAUGGUGGCA 1481 AGGGUUUU 53335_I2_251 BCL11a Intron 2 − chr2: 60495836-60495861 CUGCCCCAGGCUCCCAUG 1482 GUGGCAA 53335_I2_252 BCL11a Intron 2 − chr2: 60495837-60495862 UCUGCCCCAGGCUCCCAU 1483 GGUGGCA 53335_I2_253 BCL11a Intron 2 − chr2: 60495842-60495867 CCUUCUCUGCCCCAGGCU 1484 CCCAUGG 53335_I2_254 BCL11a Intron 2 − chr2: 60495845-60495870 GUGCCUUCUCUGCCCCA 1485 GGCUCCCA 53335_I2_255 BCL11a Intron 2 − chr2: 60495854-60495879 GACUUCACUGUGCCUUC 1486 UCUGCCCC 53335_I2_256 BCL11a Intron 2 − chr2: 60495893-60495918 AAAAAUGACAGCACCAU 1487 UUAGAGCC 53335_I2_257 BCL11a Intron 2 − chr2: 60495978-60496003 UUUCCAGAGCUGCAGUA 1488 UGUUUCUU 53335_I2_258 BCL11a Intron 2 − chr2: 60496020-60496045 GGGUGACCUCUGGAUCC 1489 CUUCUCUU 53335_I2_259 BCL11a Intron 2 − chr2: 60496035-60496060 ACUUUUCACAUAUGAGG 1490 GUGACCUC 53335_I2_260 BCL11a Intron 2 − chr2: 60496045-60496070 UUAUCAAUUGACUUUUC 1491 ACAUAUGA 53335_I2_261 BCL11a Intron 2 − chr2: 60496046-60496071 AUUAUCAAUUGACUUUU 1492 CACAUAUG 53335_I2_262 BCL11a Intron 2 − chr2: 60496090-60496115 GCAUUGCUUUCAAUCAU 1493 CUCCCCUC 53335_I2_263 BCL11a Intron 2 − chr2: 60496119-60496144 UGUUUCCGUAAUCCAUU 1494 UCCUGCAC 53335_I2_264 BCL11a Intron 2 − chr2: 60496165-60496190 AGAACUUUCCCGGUUCU 1495 GGUUUUCU 53335_I2_265 BCL11a Intron 2 − chr2: 60496166-60496191 CAGAACUUUCCCGGUUC 1496 UGGUUUUC 53335_I2_266 BCL11a Intron 2 − chr2: 60496174-60496199 CCGACUUCCAGAACUUU 1497 CCCGGUUC 53335_I2_267 BCL11a Intron 2 − chr2: 60496180-60496205 GUUUUUCCGACUUCCAG 1498 AACUUUCC 53335_I2_268 BCL11a Intron 2 − chr2: 60496233-60496258 GACAAGGCAUUCUGUAA 1499 ACGUGUAU

In embodiments, the gRNA targeting domain consists of the 20 3′ nt of any one of the sequences in the table above.

Exemplary preferred gRNA targeting domains useful in the compositions and methods of the invention are described in the tables below.

TABLE 5 Preferred Guide RNA Targeting Domains Directed to Coding Regions of the BCL11a Gene SEQ ID Id. Target gRNA Targeting Domain Targeting Site (Chr2) NO: CR000044 BCL11a ACAGGCCGUGAACCUAAGUG 60678414-60678436 1 CR000056 BCL11a UAGAGGGGGGAAAUUAUAGG 60678685-60678707 2 CR000068 BCL11a CGAGCGGUAAAUCCUAAAGA 60678840-60678862 3 CR000079 BCL11a AGACAAAUUCAAAUCCUGCA 60678895-60678917 4 CR000091 BCL11a GCUUUUGGUGGCUACCAUGC 60678909-60678931 5 CR000102 BCL11a AAUUUAUGCCAUCUGAUAAG 60679112-60679134 6 CR000033 BCL11a UGUUCCUCCUACCCACCCGA 60679178-60679200 7 CR000045 BCL11a AUAAAUGUUGGAGCUUUAGG 60679288-60679310 8 CR000069 BCL11a CAACCUAAUUACCUGUAUUG 60679389-60679411 9 CR000080 BCL11a CGCUGUCAUGAGUGAUGCCC 60679428-60679450 10 CR000092 BCL11a GGCAUCACUCAUGACAGCGA 60679432-60679454 11 CR000103 BCL11a AGUCCCAUAGAGAGGGCCCG 60679456-60679478 12 CR000115 BCL11a ACUGAUUCACUGUUCCAAUG 60679476-60679498 13 CR000034 BCL11a AGGACUCUGUCUUCGCACAA 60679577-60679599 14 CR000058 BCL11a CCACGCUGACGUCGACUGGG 60679650-60679672 15 CR000070 BCL11a GUUCUUCACACACCCCCAUU 60679779-60679801 16 CR000081 BCL11a GCGCUUCUCCACACCGCCCG 60687934-60687956 17 CR000093 BCL11a GUCUGGAGUCUCCGAAGCUA 60688006-60688028 18 CR000116 BCL11a AAAGAUCCCUUCCUUAGCUU 60688017-60688039 19 CR000035 BCL11a UCGCCGGCUACGCGGCCUCC 60688046-60688068 20 CR000047 BCL11a CGGAGAACGUGUACUCGCAG 60688070-60688092 21 CR000071 BCL11a GAGCUUGAUGCGCUUAGAGA 60688133-60688155 22 CR000082 BCL11a CCCCCCGAGGCCGACUCGCC 60688200-60688222 23 CR000094 BCL11a CACCAUGCCCUGCAUGACGU 60688394-60688416 24 CR000105 BCL11a GAGAGCGAGAGGGUGGACUA 60688506-60688528 25 CR000117 BCL11a CACGGACUUGAGCGCGCUGC 60688649-60688671 26 CR000036 BCL11a GCCCACCAAGUCGCUGGUGC 60688676-60688698 27 CR000048 BCL11a CCCACCAAGUCGCUGGUGCC 60688677-60688699 28 CR000060 BCL11a GGCGGUGGAGAGACCGUCGU 60688712-60688734 29 CR000072 BCL11a GCCGCAGAACUCGCAUGACU 60688898-60688920 30 CR000083 BCL11a CCGCCCCCAGGCGCUCUAUG 60689194-60689216 31 CR000095 BCL11a UGGGGGUCCAAGUGAUGUCU 60689217-60689239 32 CR000106 BCL11a CUCAACUUACAAAUACCCUG 60695857-60695879 33 CR000118 BCL11a AGUGCAGAAUAUGCCCCGCA 60695872-60695894 34 CR000037 BCL11a GCAUAUUCUGCACUCAUCCC 60695881-60695903 35 CR000049 BCL11a GAGCUCUAAUCCCCACGCCU 60695898-60695920 36 CR000061 BCL11a AGAGCUCCAUGUGCAGAACG 60695914-60695936 37 CR000084 BCL11a GAUAAACUUCUGCACUGGAG 60695947-60695969 38 CR000096 BCL11a UAGCUGUAGUGCUUGAUUUU 60695981-60696003 39 CR000107 BCL11a UAUCCAAAUUCAUACAAUAG 60716451-60716473 40 CR000119 BCL11a AUGCCCUGAGUAUCCCAACA 60717068-60717090 41 CR000038 BCL11a UAGUAACAGACCCAUGUGCU 60717232-60717254 42 CR000050 BCL11a AUACUUCAAGGCCUCAAUGA 60717661-60717683 43 CR000062 BCL11a GACUAGGUAGACCUUCAUUG 60717672-60717694 44 CR000073 BCL11a CUGAGCUAGUGGGGGCUCUU 60720773-60720795 45 CR000085 BCL11a CUGAGCACAUUCUUACGCCU 60721291-60721313 46 CR000097 BCL11a UUUAUAAGACAUUAGGGUAt 60721534-60721556 47 CR000108 BCL11a UGAUAGGUGCCUAUAUGUGA 60722096-60722118 48 CR000120 BCL11a UCCACCCAUCCAUCACAUAU 60722105-60722127 49 CR000039 BCL11a CUUCAAAGUUGUAUUGACCC 60722434-60722456 50 CR000051 BCL11a AAACCAGACUAGUUUAUAGG 60722687-60722709 51 CR000063 BCL11a UUUGAGACAGUUACCCCUUC 60723706-60723728 52 CR000074 BCL11a AACCUGAGGGCUAGUUUCUA 60724541-60724563 53 CR000086 BCL11a GCCUGGACCCACCGCUUCAU 60725058-60725080 54 CR000109 BCL11a AAACCAGUGAGGUCAUCUAU 60725857-60725879 55 CR000121 BCL11a ACCUGCUAUGUGUUCCUGUU 60773104-60773126 56 CR000040 BCL11a UAGAGGAAUUUGCCCCAAAC 60773118-60773140 57 CR000052 BCL11a GAUAAACAAUCGUCAUCCUC 60773150-60773172 58 CR000064 BCL11a UGGCAUCCAGGUCACGCCAG 60773166-60773188 59 CR000075 BCL11a GACCUGGAUGCCAACCUCCA 60773176-60773198 60 CR000087 BCL11a AAAAGCAUCCAAUCCCGUGG 60773190-60773212 61 CR000110 BCL11a GAUGCUUUUUUCAUCUCGAU 60773204-60773226 62 CR000122 BCL11a CCACAGCUUUUUCUAAGCAG 60773247-60773269 63 CR000041 BCL11a CCCCCAAUGGGAAGUUCAUC 60773316-60773338 64 CR000053 BCL11a AUCAUGACCUCCUCACCUGU 60773344-60773366 65 CR000065 BCL11a AGGAGGUCAUGAUCCCCUUC 60773354-60773376 66 CR000088 BCL11a CCCCUUCUGGAGCUCCCAAC 60773367-60773389 67 CR000099 BCL11a GCUCCCAACGGGCCGUGGUC 60773378-60773400 68 CR000111 BCL11a ACAGAUGAUGAACCAGACCA 60773390-60773412 69 CR000123 BCL11a UCUGUAAGAAUGGCUUCAAG 60773408-60773430 70 CR000042 BCL11a CAAUUAUUAGAGUGCCAGAG 60773459-60773481 71 CR000054 BCL11a GCCUUGCUUGCGGCGAGACA 60780385-60780407 72 CR000066 BCL11a ACCAUGUCUCGCCGCAAGCA 60780386-60780408 73 CR000077 BCL11a GAGUCUCCUUCUUUCUAACC 60780482-60780504 74 CR000089 BCL11a GAAUUGUGGGAGAGCCGUCA 60780582-60780604 75 CR000100 BCL11a AAAAUAGAGCGAGAGUGCAC 60781166-60781188 76 CR000112 BCL11a GCCCCUGGCGUCCACACGCG 60781306-60781328 77 CR000124 BCL11a CUCCUCGUUCUUUAUUCCUC 60781716-60781738 78 CR000043 BCL11a GACUGCCCGCGCUUUGUCCU 60781815-60781837 79 CR000055 BCL11a UUCCCAGGGACUGGGACUCC 60781838-60781860 80 CR000078 BCL11a UGGCUCCUGGGUGUGCGCCU 60782123-60782145 81 CR000090 BCL11a UGAAGCCCGCUUUUUGACAG 60782254-60782276 82 CR000101 BCL11a AGGGUGGAGACGGGUCGCCA 60782526-60782548 83 CR000113 BCL11a GCUCAGGGUCUCGCGGGCCA 60782543-60782565 84 CR000059 BCL11a UGAGUCCGAGCAGAAGAAGA 73160981-73161003 85

TABLE 6 Preferred Guide RNA Targeting Domains directed to the French HPFH (French HPFH; Sankaran VG et al. A functional element necessary for fetal hemoglobin silencing. NEJM (2011) 365: 807-814.) SEQ Target Genomic Target ID Id. Name Strand gRNA Targeting Domain Location NO: CR001016 HPFH − UCUUAAACCAACCUGCUCAC chr11: 5234538-5234558 86 CR001017 HPFH + CAGGUUGGUUUAAGAUAAGC chr11: 5234543-5234563 87 CR001018 HPFH + AGGUUGGUUUAAGAUAAGCA chr11: 5234544-5234564 88 CR001019 HPFH − UUAAGGGAAUAGUGGAAUGA chr11: 5234600-5234620 89 CR001020 HPFH − AGGGCAAGUUAAGGGAAUAG chr11: 5234608-5234628 90 CR001021 HPFH + CCCUUAACUUGCCCUGAGAU chr11: 5234613-5234633 91 CR001022 HPFH − CCAAUCUCAGGGCAAGUUAA chr11: 5234616-5234636 92 CR001023 HPFH − GCCAAUCUCAGGGCAAGUUA chr11: 5234617-5234637 93 CR001024 HPFH − UGACAGAACAGCCAAUCUCA chr11: 5234627-5234647 94 CR001025 HPFH − AUGACAGAACAGCCAAUCUC chr11: 5234628-5234648 95 CR001026 HPFH − GAGAUAUGUAGAGGAGAACA chr11: 5234670-5234690 96 CR001027 HPFH − GGAGAUAUGUAGAGGAGAAC chr11: 5234671-5234691 97 CR001028 HPFH − UGCGGUGGGGAGAUAUGUAG chr11: 5234679-5234699 98 CR001029 HPFH − CUGCUGAAAGAGAUGCGGUG chr11: 5234692-5234712 99 CR001030 HPFH − ACUGCUGAAAGAGAUGCGGU chr11: 5234693-5234713 100 CR001031 HPFH − AACUGCUGAAAGAGAUGCGG chr11: 5234694-5234714 101 CR001032 HPFH − AACAACUGCUGAAAGAGAUG chr11: 5234697-5234717 102 CR001033 HPFH − UCUGCAAAAAUGAAACUAGG chr11: 5234731-5234751 103 CR001034 HPFH − ACUUCUGCAAAAAUGAAACU chr11: 5234734-5234754 104 CR001035 HPFH + CAUUUUUGCAGAAGUGUUUU chr11: 5234739-5234759 105 CR001036 HPFH + AGUGUUUUAGGCUAAUAUAG chr11: 5234751-5234771 106 CR001037 HPFH − UUGGAGACAAAAAUCUCUAG chr11: 5234883-5234903 107 CR001038 HPFH + UCUAGAGAUUUUUGUCUCCA chr11: 5234882-5234902 108 CR001039 HPFH + CUAGAGAUUUUUGUCUCCAA chr11: 5234883-5234903 109 CR001040 HPFH + GUCUCCAAGGGAAUUUUGAG chr11: 5234895-5234915 110 CR001041 HPFH + CCAAGGGAAUUUUGAGAGGU chr11: 5234899-5234919 111 CR001042 HPFH − CCAACCUCUCAAAAUUCCCU chr11: 5234902-5234922 112 CR001043 HPFH + GGAAUUUUGAGAGGUUGGAA chr11: 5234904-5234924 113 CR001044 HPFH + UGCUUGCUUCCUCCUUCUUU chr11: 5234953-5234973 114 CR001045 HPFH − AAGAAUUUACCAAAAGAAGG chr11: 5234965-5234985 115 CR001046 HPFH − AGGAAGAAUUUACCAAAAGA chr11: 5234968-5234988 116 CR001047 HPFH − AAAAAUUAGAGUUUUAUUAU chr11: 5234988-5235008 117 CR001048 HPFH − UUUUUUAAAUAUUCUUUUAA Chr11: 5235023-5235045 118 CR001049 HPFH + UAUUUACCAGUUAUUGAAAU chr11: 5235062-5235082 119 CR001050 HPFH + CCAGUUAUUGAAAUAGGUUC chr11: 5235068-5235088 120 CR001051 HPFH − CCAGAACCUAUUUCAAUAAC chr11: 5235071-5235091 121 CR001052 HPFH + UUCUGGAAACAUGAAUUUUA chr11: 5235085-5235105 122 CR001053 HPFH + AUUUUGAAUGUUUAAAAUUA chr11: 5235151-5235171 123 CR001054 HPFH − AAAUUUAAUCUGGCUGAAUA chr11: 5235216-5235236 124 CR001055 HPFH − GAACUUCGUUAAAUUUAAUC chr11: 5235226-5235246 125 CR001056 HPFH + AUUAAAUUUAACGAAGUUCC chr11: 5235227-5235247 126 CR001057 HPFH + UUAAAUUUAACGAAGUUCCU chr11: 5235228-5235248 127 CR001058 HPFH − UUCUGUACUAGCAUAUUCCC chr11: 5235248-5235268 128 CR001059 HPFH + UGUGUUCUUAAAAAAAAAUG Chr11: 5235275-5235297 129 CR001060 HPFH + AAAAAUGUGGAAUUAGACCC chr11: 5235293-5235313 130 CR001061 HPFH − CUACUGGGAUCUUCAUUCCU chr11: 5235313-5235333 131 CR001062 HPFH − ACUACUGGGAUCUUCAUUCC chr11: 5235314-5235334 132 CR001063 HPFH − GAAAAGAGUGAAAAACUACU chr11: 5235328-5235348 133 CR001064 HPFH − AGAAAAGAGUGAAAAACUAC chr11: 5235329-5235349 134 CR001065 HPFH + GAAUUCAAAUAAUGCCACAA chr11: 5235349-5235369 135 CR001066 HPFH − UGUGUAUUUGUCUGCCAUUG chr11: 5235366-5235386 136 CR001067 HPFH + CACCCAUGAGCAUAUCCAAA chr11: 5235384-5235404 137 CR001068 HPFH − UUCCUUUUGGAUAUGCUCAU chr11: 5235389-5235409 138 CR001069 HPFH − CUUCCUUUUGGAUAUGCUCA chr11: 5235390-5235410 139 CR001070 HPFH + CAUGAGCAUAUCCAAAAGGA chr11: 5235388-5235408 140 CR001071 HPFH + UAUCCAAAAGGAAGGAUUGA chr11: 5235396-5235416 141 CR001072 HPFH − UUUCCUUCAAUCCUUCCUUU chr11: 5235402-5235422 142 CR001073 HPFH + AAGGAAGGAUUGAAGGAAAG chr11: 5235403-5235423 143 CR001074 HPFH + GAAGGAUUGAAGGAAAGAGG chr11: 5235406-5235426 144 CR001075 HPFH + GAGGAGGAAGAAAUGGAGAA chr11: 5235422-5235442 145 CR001076 HPFH + AGGAAGAAAUGGAGAAAGGA chr11: 5235426-5235446 146 CR001077 HPFH + GAAGGAAGAGGGGAAGAGAG chr11: 5235448-5235468 147 CR001078 HPFH + GAAGAGGGGAAGAGAGAGGA chr11: 5235452-5235472 148 CR001079 HPFH + AGGGGAAGAGAGAGGAUGGA chr11: 5235456-5235476 149 CR001080 HPFH + GGGGAAGAGAGAGGAUGGAA chr11: 5235457-5235477 150 CR001081 HPFH + AAGAGAGAGGAUGGAAGGGA chr11: 5235461-5235481 151 CR001082 HPFH + AGAGAGGAUGGAAGGGAUGG chr11: 5235464-5235484 152 CR001083 HPFH + GGAAGGGAUGGAGGAGAAGA chr11: 5235473-5235493 153 CR001084 HPFH + GAAGAAGGAAAAAUAAAUAA Chr11: 5235483-5235505 154 CR001085 HPFH + AGGAAAAAUAAAUAAUGGAG Chr11: 5235488-5235510 155 CR001086 HPFH + AAAUAAAUAAUGGAGAGGAG chr11: 5235498-5235518 156 CR001087 HPFH + UGGAGAGGAGAGGAGAAAAA chr11: 5235508-5235528 157 CR001088 HPFH + AGAGGAGAGGAGAAAAAAGG chr11: 5235511-5235531 158 CR001089 HPFH + GAGGAGAGGAGAAAAAAGGA chr11: 5235512-5235532 159 CR001090 HPFH + AGGAGAGGAGAAAAAAGGAG chr11: 5235513-5235533 160 CR001091 HPFH + AGGAGAAAAAAGGAGGGGAG chr11: 5235518-5235538 161 CR001092 HPFH + GAGAGGAGAGGAGAAGGGAU chr11: 5235535-5235555 162 CR001093 HPFH + AGAGGAGAGGAGAAGGGAUA chr11: 5235536-5235556 163 CR001094 HPFH + GAAGAGAAAGAGAAAGGGAA Chr11: 5235553-5235575 164 CR001095 HPFH + AAGAGAGGAAAGAAGAGAAG chr11: 5235581-5235601 165 CR001096 HPFH + GAGAGAAAAGAAACGAAGAG Chr11: 5235598-5235620 166 CR001097 HPFH + AGAGAAAAGAAACGAAGAGA Chr11: 5235599-5235621 167 CR001098 HPFH + GAGAAAAGAAACGAAGAGAG Chr11: 5235600-5235622 168 CR001099 HPFH + AAAGAAACGAAGAGAGGGGA chr11: 5235609-5235629 169 CR001100 HPFH + AAGAAACGAAGAGAGGGGAA chr11: 5235610-5235630 170 CR001101 HPFH + GGAAGGGAAGGAAAAAAAAG chr11: 5235626-5235646 171 CR001102 HPFH + AAGACUGACAGUUCAAAUUU chr11: 5235672-5235692 172 CR001103 HPFH + ACUGACAGUUCAAAUUUUGG chr11: 5235675-5235695 173 CR001104 HPFH + UUCAAAUUUUGGUGGUGAUA chr11: 5235683-5235703 174 CR001105 HPFH + AAUAGAAACUCAAACUCUGU chr11: 5235709-5235729 175 CR001106 HPFH + GUACAAUAGUAUAACCCCUU chr11: 5235739-5235759 176 CR001107 HPFH − CUAUUAAAGGUUUUCCAAAG chr11: 5235756-5235776 177 CR001108 HPFH − ACUAUUAAAGGUUUUCCAAA chr11: 5235757-5235777 178 CR001109 HPFH − UACUAUUAAAGGUUUUCCAA chr11: 5235758-5235778 179 CR001110 HPFH − GCAUUUGUGGAUACUAUUAA chr11: 5235769-5235789 180 CR001111 HPFH + UUAAUAGUAUCCACAAAUGC chr11: 5235769-5235789 181 CR001132 HPFH − UAUCAAGCAUCCAGCAUUUG chr11: 5235782-5235802 1500 CR001133 HPFH − UAUCUAAAAAUGUAAUUGCU chr11: 5235814-5235834 1501 CR001134 HPFH − AGCAUUUCUAUACAUGUCUU chr11: 5235862-5235882 1502 CR001135 HPFH + UAAUCAUAAAAACCUCAAAC chr11: 5235893-5235913 1503 CR001136 HPFH − UUUAAGUGGCUACCGGUUUG chr11: 5235908-5235928 1504 CR001137 HPFH − GUAAGCAUUUAAGUGGCUAC chr11: 5235915-5235935 1505 CR001138 HPFH − ACUGUUGGUAAGCAUUUAAG chr11: 5235922-5235942 1506 CR001139 HPFH − UAAUUUAUCAAUUCUACUGU chr11: 5235937-5235957 1507 CR001140 HPFH + ACAGUAGAAUUGAUAAAUUA chr11: 5235937-5235957 1508 CR001141 HPFH + CAAAUGCAUUUUACAGCAUU chr11: 5236027-5236047 1509 CR001142 HPFH + GGUUGAUUAAAAGUAACCAG chr11: 5236048-5236068 1510 CR001143 HPFH − AUAUAGUUUGAACUCACCUC Chr11: 5236059-5236081 1511 CR001144 HPFH + UUUAUUUGUAUAUAGAAAGA chr11: 5236090-5236110 1512 CR001145 HPFH + UGCCUGAGAUUCUGAUCACA chr11: 5236119-5236139 1513 CR001146 HPFH + GCCUGAGAUUCUGAUCACAA chr11: 5236120-5236140 1514 CR001147 HPFH + CCUGAGAUUCUGAUCACAAG chr11: 5236121-5236141 1515 CR001148 HPFH − CCCCUUGUGAUCAGAAUCUC chr11: 5236124-5236144 1516 CR001149 HPFH + AAGGGGAAAUGUUAUAAAAU chr11: 5236138-5236158 1517 CR001150 HPFH + AGGGGAAAUGUUAUAAAAUA chr11: 5236139-5236159 1518 CR001151 HPFH + UGUUAUAAAAUAGGGUAGAG chr11: 5236147-5236167 1519 CR001152 HPFH − CAAAGUUUAAAGGUCAUUCA chr11: 5236175-5236195 1520 CR001153 HPFH − UAACUUGUAACAAAGUUUAA chr11: 5236185-5236205 1521 CR001154 HPFH + CAAGUUAUUUUUCUGUAACC chr11: 5236198-5236218 1522 CR001155 HPFH − AAUAUCUUUCGUUGGCUUCC chr11: 5236219-5236239 1523 CR001156 HPFH − AAUUAUUCAAUAUCUUUCGU chr11: 5236227-5236247 1524 CR001157 HPFH + GAUAUUGAAUAAUUCAAGAA chr11: 5236233-5236253 1525 CR001158 HPFH + AUUGAAUAAUUCAAGAAAGG chr11: 5236236-5236256 1526 CR001159 HPFH + GAAUAAUUCAAGAAAGGUGG chr11: 5236239-5236259 1527 CR001160 HPFH + AUUCAAGAAAGGUGGUGGCA chr11: 5236244-5236264 1528 CR001161 HPFH + UAUUUUAGAAGUAGAGAAAA chr11: 5236313-5236333 1529 CR001162 HPFH + AUUUUAGAAGUAGAGAAAAU chr11: 5236314-5236334 1530 CR001163 HPFH + GAAAAUGGGAGACAAAUAGC chr11: 5236328-5236348 1531 CR001164 HPFH + AAAAUGGGAGACAAAUAGCU chr11: 5236329-5236349 1532 CR001165 HPFH + AGCUGGGCUUCUGUUGCAGU chr11: 5236345-5236365 1533 CR001166 HPFH + GCUGGGCUUCUGUUGCAGUA chr11: 5236346-5236366 1534 CR001167 HPFH + GCCAUUUCUAUUAUCAGACU chr11: 5236383-5236403 1535 CR001168 HPFH − UCCAAGUCUGAUAAUAGAAA chr11: 5236387-5236407 1536 CR001169 HPFH + UUAUCAGACUUGGACCAUGA chr11: 5236393-5236413 1537 CR001170 HPFH − CACGACUGACAUCACCGUCA chr11: 5236410-5236430 1538 CR001171 HPFH + UCAGUCGUGAACACAAGAAU chr11: 5236421-5236441 1539 CR001172 HPFH + CAGUCGUGAACACAAGAAUA chr11: 5236422-5236442 1540 CR001173 HPFH + GGCCACAUUUGUGAGUUUAG chr11: 5236443-5236463 1541 CR001174 HPFH − UACCACUAAACUCACAAAUG chr11: 5236448-5236468 1542 CR001175 HPFH + UAAAAUCAGAAAUACAGUCU chr11: 5236471-5236491 1543 CR001176 HPFH + AAAAGAUGUACUUAGAUAUG chr11: 5236528-5236548 1544 CR001177 HPFH + UGUACUUAGAUAUGUGGAUC chr11: 5236534-5236554 1545 CR001178 HPFH + AGCUCAGAAAGAAUACAACC chr11: 5236557-5236577 1546 CR001179 HPFH + ACCAGGUCAAGAAUACAGAA chr11: 5236574-5236594 1547 CR001180 HPFH − UCCAUUCUGUAUUCUUGACC chr11: 5236578-5236598 1548 CR001181 HPFH − CUGUCAUUUUUAACAGGUAG chr11: 5236646-5236666 1549 CR001182 HPFH − CAUCAUCUGUCAUUUUUAAC chr11: 5236652-5236672 1550 CR001183 HPFH − AAACACAUUCUAAGAUUUUA chr11: 5236691-5236711 1551 CR001184 HPFH + AAUCUUAGAAUGUGUUUGUG chr11: 5236694-5236714 1552 CR001185 HPFH + AUCUUAGAAUGUGUUUGUGA chr11: 5236695-5236715 1553 CR001186 HPFH + UUAGAAUGUGUUUGUGAGGG chr11: 5236698-5236718 1554 CR001187 HPFH − CAAUUUUCUUAUAUAUGAAU chr11: 5236734-5236754 1555 CR001188 HPFH + UUGAUUCUAAAAAAAAUGUU Chr11: 5236746-5236768 1556 CR001189 HPFH + AAAUGUUAGGUAAAUUCUUA chr11: 5236764-5236784 1557 CR001190 HPFH + GGUAAAUUCUUAAGGCCAUG chr11: 5236772-5236792 1558 CR001191 HPFH − AGAUCAAAUAACAGUCCUCA chr11: 5236790-5236810 1559 CR001192 HPFH + GUCUGUUAAUUCCAAAGACU chr11: 5236812-5236832 1560 CR001193 HPFH − AAAGUGAAAAGCCAAGUCUU chr11: 5236826-5236846 1561 CR001194 HPFH + CCUGAAAUGAUUUUACACAU chr11: 5236858-5236878 1562 CR001195 HPFH − CCAAUGUGUAAAAUCAUUUC chr11: 5236861-5236881 1563 CR001196 HPFH + CUGAAAUGAUUUUACACAUU chr11: 5236859-5236879 1564 CR001197 HPFH + AUUUUACACAUUGGGAGAUC chr11: 5236867-5236887 1565 CR001198 HPFH + GGUUACAUGUUUAUUCUAUA chr11: 5236888-5236908 1566 CR001199 HPFH + UCUAUAUGGAUUGCAUUGAG chr11: 5236902-5236922 1567 CR001200 HPFH + AGGAUUUGUAUAACAGAAUA chr11: 5236922-5236942 1568 CR001201 HPFH + UUUUCUUUUCUCUUCUGAGA Chr11: 5236945-5236967 1569 CR001202 HPFH − GCACUCUAGCUUGGGCAAUA chr11: 5236984-5237004 1570 CR001203 HPFH − UGCACUCUAGCUUGGGCAAU chr11: 5236985-5237005 1571 CR001204 HPFH − UGCACCAUUGCACUCUAGCU Chr11: 5236985-5237007 1572 CR001205 HPFH − GCUAUUCAGGUGGCUGAGGC chr11: 5237061-5237081 1573 CR001206 HPFH + ACCUGAAUAGCUGGGACUGC Chr11: 5237065-5237087 1574 CR001207 HPFH + GCAGGCAUGCACCACACGCC Chr11: 5237083-5237105 1575 CR001208 HPFH − UACAAAAUCAGCCGGGCGUG chr11: 5237102-5237122 1576 CR001209 HPFH − GGCUUGUAAACCCAGCACUU chr11: 5237208-5237228 1577 CR001210 HPFH − CUGGCUGGAUGCGGUGGCUC chr11: 5237229-5237249 1578 CR001211 HPFH + CUGAGCCACCGCAUCCAGCC chr11: 5237227-5237247 1579 CR001212 HPFH − CUUAUCCUGGCUGGAUGCGG chr11: 5237235-5237255 1580 CR001213 HPFH + CACCGCAUCCAGCCAGGAUA chr11: 5237233-5237253 1581 CR001214 HPFH − GACCUUAUCCUGGCUGGAUG chr11: 5237238-5237258 1582 CR001215 HPFH − CUUUUAGACCUUAUCCUGGC chr11: 5237244-5237264 1583 CR001216 HPFH + GCCAGGAUAAGGUCUAAAAG chr11: 5237244-5237264 1584 CR001217 HPFH − UCCACUUUUAGACCUUAUCC chr11: 5237248-5237268 1585 CR001218 HPFH + AAUAGCAUCUACUCUUGUUC chr11: 5237271-5237291 1586 CR001219 HPFH + CUCUUGUUCAGGAAACAAUG chr11: 5237282-5237302 1587 CR001220 HPFH + GGAAACAAUGAGGACCUGAC chr11: 5237292-5237312 1588 CR001221 HPFH + GAAACAAUGAGGACCUGACU chr11: 5237293-5237313 1589 CR001222 HPFH + ACCUGACUGGGCAGUAAGAG chr11: 5237305-5237325 1590 CR001223 HPFH − ACCACUCUUACUGCCCAGUC chr11: 5237309-5237329 1591 CR001224 HPFH + AAGAGUGGUGAUUAAUAGAU chr11: 5237320-5237340 1592 CR001225 HPFH + AGAGUGGUGAUUAAUAGAUA chr11: 5237321-5237341 1593 CR001226 HPFH + AGAAUCGAACUGUUGAUUAG chr11: 5237356-5237376 1594 CR001227 HPFH + UCGAACUGUUGAUUAGAGGU chr11: 5237360-5237380 1595 CR003027 HPFH + CGAACUGUUGAUUAGAGGUA chr11: 5237361-5237381 1692 CR003028 HPFH + AUGAUUUUAAUCUGUGACCU chr11: 5237386-5237406 1693 CR003029 HPFH + UAAUCUGUGACCUUGGUGAA chr11: 5237393-5237413 1694 CR003030 HPFH + AAUCUGUGACCUUGGUGAAU chr11: 5237394-5237414 1695 CR003031 HPFH − AGCUACUUGCCCAUUCACCA chr11: 5237406-5237426 1696 CR003032 HPFH + UAGCUAUCUAAUGACUAAAA chr11: 5237421-5237441 1697 CR003033 HPFH + AUGACUAAAAUGGAAAACAC chr11: 5237431-5237451 1698 CR003034 HPFH + AAAUACCCAUGCUGAGUCUG chr11: 5237482-5237502 1699 CR003035 HPFH − AGGCACCUCAGACUCAGCAU chr11: 5237490-5237510 1700 CR003036 HPFH − UAGGCACCUCAGACUCAGCA chr11: 5237491-5237511 1701 CR003037 HPFH + GCUGAGUCUGAGGUGCCUAU chr11: 5237492-5237512 1702 CR003038 HPFH − UAUUUAUAUAGAUGUCCUAU chr11: 5237510-5237530 1703 CR003039 HPFH − CAUAUAUCAAACAAUGUACU chr11: 5237535-5237555 1704 CR003040 HPFH + CCAGUACAUUGUUUGAUAUA chr11: 5237533-5237553 1705 CR003041 HPFH − CCAUAUAUCAAACAAUGUAC chr11: 5237536-5237556 1706 CR003042 HPFH + CAGUACAUUGUUUGAUAUAU chr11: 5237534-5237554 1707 CR003043 HPFH + CAUUGUUUGAUAUAUGGGUU chr11: 5237539-5237559 1708 CR003044 HPFH + GAUAUAUGGGUUUGGCACUG chr11: 5237547-5237567 1709 CR003045 HPFH + UAUGGGUUUGGCACUGAGGU chr11: 5237551-5237571 1710 CR003046 HPFH + GGGUUUGGCACUGAGGUUGG chr11: 5237554-5237574 1711 CR003047 HPFH + GCACUGAGGUUGGAGGUCAG chr11: 5237561-5237581 1712 CR003048 HPFH + CAGAGGUUAGAAAUCAGAGU chr11: 5237578-5237598 1713 CR003049 HPFH + AGAGGUUAGAAAUCAGAGUU chr11: 5237579-5237599 1714 CR003050 HPFH + UAGAAAUCAGAGUUGGGAAU chr11: 5237585-5237605 1715 CR003051 HPFH + AGAAAUCAGAGUUGGGAAUU chr11: 5237586-5237606 1716 CR003052 HPFH + GUUGGGAAUUGGGAUUAUAC chr11: 5237596-5237616 1717 CR003053 HPFH − CUUUGUAUUCAUCACACUCU chr11: 5237654-5237674 1718 CR003054 HPFH + AUGAAUACAAAGUUAAAUGA chr11: 5237662-5237682 1719 CR003055 HPFH − UAAAUGUUGGUGUUCAUUAA chr11: 5237689-5237709 1720 CR003056 HPFH − UGAGAUUUCACAUUAAAUGU chr11: 5237702-5237722 1721 CR003057 HPFH + ACAUUUAAUGUGAAAUCUCA chr11: 5237702-5237722 1722 CR003058 HPFH − UAAAAUCAUCGGGGAUUUUG chr11: 5237749-5237769 1723 CR003059 HPFH − CUAAAAUCAUCGGGGAUUUU chr11: 5237750-5237770 1724 CR003060 HPFH − UCUAAAAUCAUCGGGGAUUU chr11: 5237751-5237771 1725 CR003061 HPFH − ACUGAGUUCUAAAAUCAUCG chr11: 5237758-5237778 1726 CR003062 HPFH − UACUGAGUUCUAAAAUCAUC chr11: 5237759-5237779 1727 CR003063 HPFH − AUACUGAGUUCUAAAAUCAU chr11: 5237760-5237780 1728 CR003064 HPFH + UAAUUAGUGUAAUGCCAAUG chr11: 5237786-5237806 1729 CR003065 HPFH + AAUUAGUGUAAUGCCAAUGU chr11: 5237787-5237807 1730 CR003066 HPFH + AAUGCCAAUGUGGGUUAGAA chr11: 5237796-5237816 1731 CR003067 HPFH − ACUUCCAUUCUAACCCACAU chr11: 5237803-5237823 1732 CR003068 HPFH + AAUGGAAGUCAACUUGCUGU chr11: 5237814-5237834 1733 CR003069 HPFH + CUUGCUGUUGGUUUCAGAGC chr11: 5237826-5237846 1734 CR003070 HPFH + CUGUUGGUUUCAGAGCAGGU chr11: 5237830-5237850 1735 CR003071 HPFH + UUCAGAGCAGGUAGGAGAUA chr11: 5237838-5237858 1736 CR003072 HPFH + AGUGAAAAGCUGAAACAAAA chr11: 5237877-5237897 1737 CR003073 HPFH + AAGCUGAAACAAAAAGGAAA chr11: 5237883-5237903 1738 CR003074 HPFH + UGAAACAAAAAGGAAAAGGU chr11: 5237887-5237907 1739 CR003075 HPFH + GAAACAAAAAGGAAAAGGUA chr11: 5237888-5237908 1740 CR003076 HPFH + GGAAAAGGUAGGGUGAAAGA chr11: 5237898-5237918 1741 CR003077 HPFH + GAAAAGGUAGGGUGAAAGAU chr11: 5237899-5237919 1742 CR003078 HPFH + AAAGAUGGGAAAUGUAUGUA chr11: 5237913-5237933 1743 CR003079 HPFH + GAUGGGAAAUGUAUGUAAGG chr11: 5237916-5237936 1744 CR003080 HPFH + UGUAAGGAGGAUGAGCCACA chr11: 5237929-5237949 1745 CR003081 HPFH + GGAGGAUGAGCCACAUGGUA chr11: 5237934-5237954 1746 CR003082 HPFH + GAGGAUGAGCCACAUGGUAU chr11: 5237935-5237955 1747 CR003083 HPFH + GAUGAGCCACAUGGUAUGGG chr11: 5237938-5237958 1748 CR003084 HPFH − AGUAUACCUCCCAUACCAUG chr11: 5237947-5237967 1749 CR003085 HPFH + AUGGUAUGGGAGGUAUACUA chr11: 5237948-5237968 1750 CR003086 HPFH + GGAGGUAUACUAAGGACUCU chr11: 5237956-5237976 1751 CR003087 HPFH + GAGGUAUACUAAGGACUCUA chr11: 5237957-5237977 1752 CR003088 HPFH + ACUCUAGGGUCAGAGAAAUA chr11: 5237971-5237991 1753 CR003089 HPFH + CUCUAGGGUCAGAGAAAUAU chr11: 5237972-5237992 1754 CR003090 HPFH − AAGAAUGUGAAUUUUGUAGA chr11: 5238004-5238024 1755 CR003091 HPFH + UUCUACAAAAUUCACAUUCU chr11: 5238003-5238023 1756 CR003092 HPFH + ACAAAAUUCACAUUCUUGGC chr11: 5238007-5238027 1757 CR003093 HPFH + CAAAAUUCACAUUCUUGGCU chr11: 5238008-5238028 1758 CR003094 HPFH + UUCACAUUCUUGGCUGGGUG chr11: 5238013-5238033 1759 CR003095 HPFH + AGGGUGGAUCACCUGAUGUU chr11: 5238071-5238093 1760 CR003096 HPFH − GAUCUCGAACUCCUAACAUC chr11: 5238090-5238110 1761

In some aspects of the invention, it is preferred that the gRNA molecule to an HPFH region comprise, e.g., consist of, a targeting domain of a gRNA capable of producing at least about a 20% increase in F cells relative to control, e.g., in an assay described in Example 4. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 113. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 99. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 112. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 98. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 1580. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 106. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 1589. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 1503. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 160. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 1537. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 159. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 101. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 162. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 104. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 138. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 1536. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 1539. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 1585.

In some aspects of the invention, e.g., as indicated herein, it may be beneficial to include gRNA molecules targeting more than one, e.g., two, target sites (e.g., a first gRNA molecule and a second gRNA molecule). In some embodiments, the two target sites are both located in an HPFH region. In such aspects, any combination of more than one, e.g., two, gRNA molecules (e.g., a first gRNA molecule and a second gRNA molecule) comprising targeting domains listed in Table 6 may be used. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 100 and SEQ ID NO: 165, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 100 and SEQ ID NO: 113, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 100 and SEQ ID NO: 99, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 100 and SEQ ID NO: 112, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 100 and SEQ ID NO: 98, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 100 and SEQ ID NO: 1580, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 100 and SEQ ID NO: 106, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 100 and SEQ ID NO: 1503, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 100 and SEQ ID NO: 1589, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 100 and SEQ ID NO: 160, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 100 and SEQ ID NO: 1537, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 100 and SEQ ID NO: 159, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 100 and SEQ ID NO: 101, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 100 and SEQ ID NO: 162, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 100 and SEQ ID NO: 104, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 100 and SEQ ID NO: 138, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 100 and SEQ ID NO: 1536, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 100 and SEQ ID NO: 1539, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 100 and SEQ ID NO: 1585, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 165 and SEQ ID NO: 113, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 165 and SEQ ID NO: 99, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 165 and SEQ ID NO: 112, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 165 and SEQ ID NO: 98, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 165 and SEQ ID NO: 1580, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 165 and SEQ ID NO: 106, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 165 and SEQ ID NO: 1503, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 165 and SEQ ID NO: 1589, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 165 and SEQ ID NO: 160, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 165 and SEQ ID NO: 1537, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 165 and SEQ ID NO: 159, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 165 and SEQ ID NO: 101, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 165 and SEQ ID NO: 162, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 165 and SEQ ID NO: 104, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 165 and SEQ ID NO: 138, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 165 and SEQ ID NO: 1536, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 165 and SEQ ID NO: 1539, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 165 and SEQ ID NO: 1585, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 113 and SEQ ID NO: 165, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 113 and SEQ ID NO: 99, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 113 and SEQ ID NO: 112, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 113 and SEQ ID NO: 98, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 113 and SEQ ID NO: 1580, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 113 and SEQ ID NO: 106, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 113 and SEQ ID NO: 1503, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 113 and SEQ ID NO: 1589, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 113 and SEQ ID NO: 160, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 113 and SEQ ID NO: 1537, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 113 and SEQ ID NO: 159, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 113 and SEQ ID NO: 101, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 113 and SEQ ID NO: 162, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 113 and SEQ ID NO: 104, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 113 and SEQ ID NO: 138, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 113 and SEQ ID NO: 1536, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 113 and SEQ ID NO: 1539, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 113 and SEQ ID NO: 1585, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 99 and SEQ ID NO: 165, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 99 and SEQ ID NO: 113, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 99 and SEQ ID NO: 112, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 99 and SEQ ID NO: 98, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 99 and SEQ ID NO: 1580, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 99 and SEQ ID NO: 106, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 99 and SEQ ID NO: 1503, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 99 and SEQ ID NO: 1589, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 99 and SEQ ID NO: 160, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 99 and SEQ ID NO: 1537, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 99 and SEQ ID NO: 159, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 99 and SEQ ID NO: 101, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 99 and SEQ ID NO: 162, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 99 and SEQ ID NO: 104, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 99 and SEQ ID NO: 138, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 99 and SEQ ID NO: 1536, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 99 and SEQ ID NO: 1539, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 99 and SEQ ID NO: 1585, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 112 and SEQ ID NO: 165, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 112 and SEQ ID NO: 113, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 112 and SEQ ID NO: 99, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 112 and SEQ ID NO: 98, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 112 and SEQ ID NO: 1580, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 112 and SEQ ID NO: 106, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 112 and SEQ ID NO: 1503, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 112 and SEQ ID NO: 1589, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 112 and SEQ ID NO: 160, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 112 and SEQ ID NO: 1537, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 112 and SEQ ID NO: 159, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 112 and SEQ ID NO: 101, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 112 and SEQ ID NO: 162, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 112 and SEQ ID NO: 104, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 112 and SEQ ID NO: 138, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 112 and SEQ ID NO: 1536, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 112 and SEQ ID NO: 1539, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 112 and SEQ ID NO: 1585, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 98 and SEQ ID NO: 165, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 98 and SEQ ID NO: 113, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 98 and SEQ ID NO: 99, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 98 and SEQ ID NO: 112, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 98 and SEQ ID NO: 1580, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 98 and SEQ ID NO: 106, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 98 and SEQ ID NO: 1503, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 98 and SEQ ID NO: 1589, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 98 and SEQ ID NO: 160, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 98 and SEQ ID NO: 1537, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 98 and SEQ ID NO: 159, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 98 and SEQ ID NO: 101, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 98 and SEQ ID NO: 162, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 98 and SEQ ID NO: 104, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 98 and SEQ ID NO: 138, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 98 and SEQ ID NO: 1536, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 98 and SEQ ID NO: 1539, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 98 and SEQ ID NO: 1585, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1580 and SEQ ID NO: 165, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1580 and SEQ ID NO: 113, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1580 and SEQ ID NO: 99, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1580 and SEQ ID NO: 112, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1580 and SEQ ID NO: 98, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1580 and SEQ ID NO: 106, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1580 and SEQ ID NO: 1503, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1580 and SEQ ID NO: 1589, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1580 and SEQ ID NO: 160, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1580 and SEQ ID NO: 1537, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1580 and SEQ ID NO: 159, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1580 and SEQ ID NO: 101, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1580 and SEQ ID NO: 162, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1580 and SEQ ID NO: 104, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1580 and SEQ ID NO: 138, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1580 and SEQ ID NO: 1536, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1580 and SEQ ID NO: 1539, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1580 and SEQ ID NO: 1585, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 106 and SEQ ID NO: 165, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 106 and SEQ ID NO: 113, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 106 and SEQ ID NO: 99, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 106 and SEQ ID NO: 112, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 106 and SEQ ID NO: 98, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 106 and SEQ ID NO: 1580, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 106 and SEQ ID NO: 1503, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 106 and SEQ ID NO: 1589, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 106 and SEQ ID NO: 160, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 106 and SEQ ID NO: 1537, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 106 and SEQ ID NO: 159, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 106 and SEQ ID NO: 101, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 106 and SEQ ID NO: 162, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 106 and SEQ ID NO: 104, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 106 and SEQ ID NO: 138, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 106 and SEQ ID NO: 1536, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 106 and SEQ ID NO: 1539, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 106 and SEQ ID NO: 1585, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1503 and SEQ ID NO: 165, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1503 and SEQ ID NO: 113, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1503 and SEQ ID NO: 99, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1503 and SEQ ID NO: 112, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1503 and SEQ ID NO: 98, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1503 and SEQ ID NO: 1580, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1503 and SEQ ID NO: 106, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1503 and SEQ ID NO: 1589, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1503 and SEQ ID NO: 160, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1503 and SEQ ID NO: 1537, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1503 and SEQ ID NO: 159, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1503 and SEQ ID NO: 101, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1503 and SEQ ID NO: 162, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1503 and SEQ ID NO: 104, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1503 and SEQ ID NO: 138, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1503 and SEQ ID NO: 1536, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1503 and SEQ ID NO: 1539, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1503 and SEQ ID NO: 1585, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1589 and SEQ ID NO: 165, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1589 and SEQ ID NO: 113, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1589 and SEQ ID NO: 99, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1589 and SEQ ID NO: 112, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1589 and SEQ ID NO: 98, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1589 and SEQ ID NO: 1580, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1589 and SEQ ID NO: 106, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1589 and SEQ ID NO: 1503, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1589 and SEQ ID NO: 160, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1589 and SEQ ID NO: 1537, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1589 and SEQ ID NO: 159, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1589 and SEQ ID NO: 101, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1589 and SEQ ID NO: 162, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1589 and SEQ ID NO: 104, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1589 and SEQ ID NO: 138, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1589 and SEQ ID NO: 1536, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1589 and SEQ ID NO: 1539, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1589 and SEQ ID NO: 1585, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 160 and SEQ ID NO: 165, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 160 and SEQ ID NO: 113, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 160 and SEQ ID NO: 99, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 160 and SEQ ID NO: 112, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 160 and SEQ ID NO: 98, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 160 and SEQ ID NO: 1580, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 160 and SEQ ID NO: 106, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 160 and SEQ ID NO: 1503, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 160 and SEQ ID NO: 1589, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 160 and SEQ ID NO: 1537, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 160 and SEQ ID NO: 159, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 160 and SEQ ID NO: 101, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 160 and SEQ ID NO: 162, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 160 and SEQ ID NO: 104, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 160 and SEQ ID NO: 138, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 160 and SEQ ID NO: 1536, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 160 and SEQ ID NO: 1539, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 160 and SEQ ID NO: 1585, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1537 and SEQ ID NO: 165, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1537 and SEQ ID NO: 113, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1537 and SEQ ID NO: 99, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1537 and SEQ ID NO: 112, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1537 and SEQ ID NO: 98, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1537 and SEQ ID NO: 1580, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1537 and SEQ ID NO: 106, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1537 and SEQ ID NO: 1503, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1537 and SEQ ID NO: 1589, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1537 and SEQ ID NO: 160, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1537 and SEQ ID NO: 159, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1537 and SEQ ID NO: 101, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1537 and SEQ ID NO: 162, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1537 and SEQ ID NO: 104, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1537 and SEQ ID NO: 138, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1537 and SEQ ID NO: 1536, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1537 and SEQ ID NO: 1539, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1537 and SEQ ID NO: 1585, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 159 and SEQ ID NO: 165, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 159 and SEQ ID NO: 113, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 159 and SEQ ID NO: 99, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 159 and SEQ ID NO: 112, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 159 and SEQ ID NO: 98, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 159 and SEQ ID NO: 1580, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 159 and SEQ ID NO: 106, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 159 and SEQ ID NO: 1503, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 159 and SEQ ID NO: 1589, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 159 and SEQ ID NO: 160, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 159 and SEQ ID NO: 1537, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 159 and SEQ ID NO: 101, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 159 and SEQ ID NO: 162, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 159 and SEQ ID NO: 104, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 159 and SEQ ID NO: 138, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 159 and SEQ ID NO: 1536, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 159 and SEQ ID NO: 1539, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 159 and SEQ ID NO: 1585, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 101 and SEQ ID NO: 165, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 101 and SEQ ID NO: 113, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 101 and SEQ ID NO: 99, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 101 and SEQ ID NO: 112, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 101 and SEQ ID NO: 98, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 101 and SEQ ID NO: 1580, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 101 and SEQ ID NO: 106, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 101 and SEQ ID NO: 1503, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 101 and SEQ ID NO: 1589, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 101 and SEQ ID NO: 160, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 101 and SEQ ID NO: 1537, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 101 and SEQ ID NO: 159, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 101 and SEQ ID NO: 162, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 101 and SEQ ID NO: 104, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 101 and SEQ ID NO: 138, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 101 and SEQ ID NO: 1536, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 101 and SEQ ID NO: 1539, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 101 and SEQ ID NO: 1585, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 162 and SEQ ID NO: 165, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 162 and SEQ ID NO: 113, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 162 and SEQ ID NO: 99, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 162 and SEQ ID NO: 112, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 162 and SEQ ID NO: 98, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 162 and SEQ ID NO: 1580, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 162 and SEQ ID NO: 106, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 162 and SEQ ID NO: 1503, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 162 and SEQ ID NO: 1589, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 162 and SEQ ID NO: 160, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 162 and SEQ ID NO: 1537, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 162 and SEQ ID NO: 159, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 162 and SEQ ID NO: 101, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 104 and SEQ ID NO: 165, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 104 and SEQ ID NO: 113, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 104 and SEQ ID NO: 99, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 104 and SEQ ID NO: 112, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 104 and SEQ ID NO: 98, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 104 and SEQ ID NO: 1580, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 104 and SEQ ID NO: 106, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 104 and SEQ ID NO: 1503, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 104 and SEQ ID NO: 1589, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 104 and SEQ ID NO: 160, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 104 and SEQ ID NO: 1537, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 104 and SEQ ID NO: 159, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 104 and SEQ ID NO: 101, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 104 and SEQ ID NO: 162, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 104 and SEQ ID NO: 138, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 104 and SEQ ID NO: 1536, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 104 and SEQ ID NO: 1539, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 104 and SEQ ID NO: 1585, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 138 and SEQ ID NO: 165, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 138 and SEQ ID NO: 113, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 138 and SEQ ID NO: 99, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 138 and SEQ ID NO: 112, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 138 and SEQ ID NO: 98, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 138 and SEQ ID NO: 1580, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 138 and SEQ ID NO: 106, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 138 and SEQ ID NO: 1503, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 138 and SEQ ID NO: 1589, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 138 and SEQ ID NO: 160, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 138 and SEQ ID NO: 1537, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 138 and SEQ ID NO: 159, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 138 and SEQ ID NO: 101, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 138 and SEQ ID NO: 162, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 138 and SEQ ID NO: 104, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 138 and SEQ ID NO: 1536, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 138 and SEQ ID NO: 1539, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 138 and SEQ ID NO: 1585, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1536 and SEQ ID NO: 165, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1536 and SEQ ID NO: 113, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1536 and SEQ ID NO: 99, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1536 and SEQ ID NO: 112, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1536 and SEQ ID NO: 98, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1536 and SEQ ID NO: 1580, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1536 and SEQ ID NO: 106, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1536 and SEQ ID NO: 1503, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1536 and SEQ ID NO: 1589, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1536 and SEQ ID NO: 160, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1536 and SEQ ID NO: 1537, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1536 and SEQ ID NO: 159, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1536 and SEQ ID NO: 101, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1536 and SEQ ID NO: 162, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1536 and SEQ ID NO: 104, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1536 and SEQ ID NO: 138, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1536 and SEQ ID NO: 1539, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1536 and SEQ ID NO: 1585, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1539 and SEQ ID NO: 165, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1539 and SEQ ID NO: 113, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1539 and SEQ ID NO: 99, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1539 and SEQ ID NO: 112, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1539 and SEQ ID NO: 98, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1539 and SEQ ID NO: 1580, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1539 and SEQ ID NO: 106, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1539 and SEQ ID NO: 1503, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1539 and SEQ ID NO: 1589, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1539 and SEQ ID NO: 160, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1539 and SEQ ID NO: 1537, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1539 and SEQ ID NO: 159, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1539 and SEQ ID NO: 101, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1539 and SEQ ID NO: 162, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1539 and SEQ ID NO: 104, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1539 and SEQ ID NO: 138, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1539 and SEQ ID NO: 1536, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1539 and SEQ ID NO: 1585, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1585 and SEQ ID NO: 165, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1585 and SEQ ID NO: 113, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1585 and SEQ ID NO: 99, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1585 and SEQ ID NO: 112, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1585 and SEQ ID NO: 98, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1585 and SEQ ID NO: 1580, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1585 and SEQ ID NO: 106, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1585 and SEQ ID NO: 1503, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1585 and SEQ ID NO: 1589, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1585 and SEQ ID NO: 160, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1585 and SEQ ID NO: 1537, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1585 and SEQ ID NO: 159, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1585 and SEQ ID NO: 101, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1585 and SEQ ID NO: 162, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1585 and SEQ ID NO: 104, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1585 and SEQ ID NO: 138, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1585 and SEQ ID NO: 1536, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1585 and SEQ ID NO: 1539, respectively.

TABLE 7 Preferred Guide RNA Targeting Domains directed to the +58 Enhancer Region of the BCL11a Gene (i.e., to a BCL11a Enhancer) Exon/ SEQ ID Id. Feature Strand Targeting domain Locations NO: CR00242 58 + UAUGCAAUUUUUGCCAAGAU Chr2: 60494419-60494441 182 CR00243 58 + UUUUGCCAAGAUGGGAGUAU Chr2: 60494427-60494449 183 CR00244 58 + UUUGCCAAGAUGGGAGUAUG Chr2: 60494428-60494450 184 CR00245 58 + UCAGUGAGAUGAGAUAUCAA Chr2: 60494477-60494499 185 CR00246 58 + CAGUGAGAUGAGAUAUCAAA Chr2: 60494478-60494500 186 CR00247 58 + CCAUCUCCCUAAUCUCCAAU Chr2: 60494518-60494540 187 CR00248 58 − CCAAUUGGAGAUUAGGGAGA Chr2: 60494518-60494540 188 CR00249 58 − GCUUUGCCAAUUGGAGAUUA Chr2: 60494524-60494546 189 CR00250 58 − GGCUUUGCCAAUUGGAGAUU Chr2: 60494525-60494547 190 CR00251 58 + AAUUGGCAAAGCCAGACUUG Chr2: 60494535-60494557 191 CR00252 58 − AGUCUGUAUUGCCCCAAGUC Chr2: 60494546-60494568 192 CR00253 58 + AGACUUGGGGCAAUACAGAC Chr2: 60494548-60494570 193 CR00255 58 − ACAUUUGGUGAUAAAUCAUU Chr2: 60494602-60494624 194 CR00256 58 + CCAAAUGUUCUUUCUUCAGC Chr2: 60494617-60494639 195 CR00257 58 + AUAAUAGUAUAUGCUUCAUA Chr2: 60494676-60494698 196 CR00258 58 − CGGAGCACUUACUCUGCUCU Chr2: 60494737-60494759 197 CR00259 58 − AGCAUUUUAGUUCACAAGCU Chr2: 60494757-60494779 198 CR00260 58 − UGUAACUAAUAAAUACCAGG Chr2: 60494781-60494803 199 CR00261 58 − AGGUGUAACUAAUAAAUACC Chr2: 60494784-60494806 200 CR00264 58 − UCUGACCCAAACUAGGAAUU Chr2: 60494836-60494858 201 CR00266 58 + AAGGAAAAGAAUAUGACGUC Chr2: 60494883-60494905 202 CR00267 58 + AGGAAAAGAAUAUGACGUCA Chr2: 60494884-60494906 203 CR00268 58 + GGAAAAGAAUAUGACGUCAG Chr2: 60494885-60494907 204 CR00269 58 + GAAAAGAAUAUGACGUCAGG Chr2: 60494886-60494908 205 CR00270 58 + UCAGGGGGAGGCAAGUCAGU Chr2: 60494901-60494923 206 CR00271 58 + CAGGGGGAGGCAAGUCAGUU Chr2: 60494902-60494924 207 CR00272 58 AUCACAUAUAGGCACCUAUC Chr2: 60494939-60494961 208 CR00273 58 CAGGUACCAGCUACUGUGUU Chr2: 60494939-60494961 209 CR00274 58 ACUAUCCACGGAUAUACACU Chr2: 60494939-60494961 210 CR00275 58 + CACAGUAGCUGGUACCUGAU Chr2: 60494939-60494961 211 CR00276 58 − AUCACAUAUAGGCACCUAUC Chr2: 60494953-60494975 212 CR00277 58 + UGAUAGGUGCCUAUAUGUGA Chr2: 60494955-60494977 213 CR00278 58 + AGGUGCCUAUAUGUGAUGGA Chr2: 60494959-60494981 214 CR00279 58 + GGUGCCUAUAUGUGAUGGAU Chr2: 60494960-60494982 215 CR00280 58 − UCCACCCAUCCAUCACAUAU Chr2: 60494964-60494986 216 CR00281 58 + ACAGCCCGACAGAUGAAAAA Chr2: 60494986-60495008 217 CR00282 58 + AUGAAAAAUGGACAAUUAUG Chr2: 60494998-60495020 218 CR00283 58 + AAAAAUGGACAAUUAUGAGG Chr2: 60495001-60495023 219 CR00284 58 + AAAAUGGACAAUUAUGAGGA Chr2: 60495002-60495024 220 CR00285 58 + AAAUGGACAAUUAUGAGGAG Chr2: 60495003-60495025 221 CR00286 58 + GAGGAGGGGAGAGUGCAGAC Chr2: 60495017-60495039 222 CR00287 58 + AGGAGGGGAGAGUGCAGACA Chr2: 60495018-60495040 223 CR00288 58 + CUUCACCUCCUUUACAAUUU Chr2: 60495045-60495067 224 CR00289 58 + UUCACCUCCUUUACAAUUUU Chr2: 60495046-60495068 225 CR00290 58 − GACUCCCAAAAUUGUAAAGG Chr2: 60495050-60495072 226 CR00291 58 − GUGGACUCCCAAAAUUGUAA Chr2: 60495053-60495075 227 CR00292 58 + UUUUGGGAGUCCACACGGCA Chr2: 60495062-60495084 228 CR00293 58 − AAUUUGUAUGCCAUGCCGUG Chr2: 60495072-60495094 229 CR00294 58 + CCAAGAGAGCCUUCCGAAAG Chr2: 60495135-60495157 230 CR00295 58 − CCAGGGGGGCCUCUUUCGGA Chr2: 60495144-60495166 231 CR00296 58 + CCUUCCGAAAGAGGCCCCCC Chr2: 60495144-60495166 232 CR00297 58 + CUUCCGAAAGAGGCCCCCCU Chr2: 60495145-60495167 233 CR00298 58 + AAGAGGCCCCCCUGGGCAAA Chr2: 60495152-60495174 234 CR00299 58 − CGGUGGCCGUUUGCCCAGGG Chr2: 60495158-60495180 235 CR00300 58 − UCGGUGGCCGUUUGCCCAGG Chr2: 60495159-60495181 236 CR00301 58 − AUCGGUGGCCGUUUGCCCAG Chr2: 60495160-60495182 237 CR00302 58 − CAUCGGUGGCCGUUUGCCCA Chr2: 60495161-60495183 238 CR00303 58 + CCUGGGCAAACGGCCACCGA Chr2: 60495162-60495184 239 CR00304 58 − CCAUCGGUGGCCGUUUGCCC Chr2: 60495162-60495184 240 CR00305 58 + GCAAACGGCCACCGAUGGAG Chr2: 60495167-60495189 241 CR00306 58 − CUGGCAGACCUCUCCAUCGG Chr2: 60495175-60495197 242 CR00307 58 − GGACUGGCAGACCUCUCCAU Chr2: 60495178-60495200 243 CR00308 58 − UCUGAUUAGGGUGGGGGCGU Chr2: 60495213-60495235 244 CR00309 58 + CACGCCCCCACCCUAAUCAG Chr2: 60495215-60495237 245 CR00310 58 − UUGGCCUCUGAUUAGGGUGG Chr2: 60495219-60495241 246 CR00311 58 − UUUGGCCUCUGAUUAGGGUG Chr2: 60495220-60495242 247 CR00312 58 − GUUUGGCCUCUGAUUAGGGU Chr2: 60495221-60495243 248 CR00313 58 − GGUUUGGCCUCUGAUUAGGG Chr2: 60495222-60495244 249 CR00314 58 − AAGGGUUUGGCCUCUGAUUA Chr2: 60495225-60495247 250 CR00315 58 − GAAGGGUUUGGCCUCUGAUU Chr2: 60495226-60495248 251 CR00316 58 − UUGCUUUUAUCACAGGCUCC Chr2: 60495248-60495270 252 CR00317 58 − CUAACAGUUGCUUUUAUCAC Chr2: 60495255-60495277 253 CR00318 58 + CUUCAAAGUUGUAUUGACCC Chr2: 60495293-60495315 254 CR00319 58 − ACUCUUAGACAUAACACACC Chr2: 60495311-60495333 255 CR00320 58 + UAGAUGCCAUAUCUCUUUUC Chr2: 60495333-60495355 256 CR00321 58 − CAUAGGCCAGAAAAGAGAUA Chr2: 60495339-60495361 257 CR00322 58 + GGCCUAUGUUAUUACCUGUA Chr2: 60495354-60495376 258 CR00323 58 − GUCCAUACAGGUAAUAACAU Chr2: 60495356-60495378 259 CR00324 58 + UACCUGUAUGGACUUUGCAC Chr2: 60495366-60495388 260 CR00325 58 − UUCCAGUGCAAAGUCCAUAC Chr2: 60495368-60495390 261 CR00326 58 + UGCUCUUACUUAUGCACACC Chr2: 60495400-60495422 262 CR00327 58 + GCUCUUACUUAUGCACACCU Chr2: 60495401-60495423 263 CR00328 58 + CUCUUACUUAUGCACACCUG Chr2: 60495402-60495424 264 CR00329 58 − CAGGGCUGGCUCUAUGCCCC Chr2: 60495418-60495440 265 CR00330 58 − GCUGAAAAGCGAUACAGGGC Chr2: 60495432-60495454 266 CR00331 58 − GAUGGCUGAAAAGCGAUACA Chr2: 60495436-60495458 267 CR00332 58 − AGAUGGCUGAAAAGCGAUAC Chr2: 60495437-60495459 268 CR00333 58 − GGGAGUUAUCUGUAGUGAGA Chr2: 60495454-60495476 269 CR00334 58 − AAGGCAGCUAGACAGGACUU Chr2: 60495474-60495496 270 CR00335 58 − GAAGGCAGCUAGACAGGACU Chr2: 60495475-60495497 271 CR00336 58 − GAUAAGGAAGGCAGCUAGAC Chr2: 60495481-60495503 272 CR00337 58 + CUAGCUGCCUUCCUUAUCAC Chr2: 60495486-60495508 273 CR00338 58 − UGGGUGCUAUUCCUGUGAUA Chr2: 60495497-60495519 274 CR00339 58 + UAUCACAGGAAUAGCACCCA Chr2: 60495500-60495522 275 CR00340 58 − CUGAGGUACUGAUGGACCUU Chr2: 60495516-60495538 276 CR00341 58 − UCUGAGGUACUGAUGGACCU Chr2: 60495517-60495539 277 CR001124 58 − UUAGGGUGGGGGCGUGGGUG Chr2: 60495214-60495236 334 CR001125 58 − UUUUAUCACAGGCUCCAGGA Chr2: 60495215-60495237 335 CR001126 58 − UUUAUCACAGGCUCCAGGAA Chr2: 60495216-60495238 336 CR001127 58 − CACAGGCUCCAGGAAGGGUU Chr2: 60495220-60495242 337 CR001128 58 + AUCAGAGGCCAAACCCUUCC Chr2: 60495236-60495258 338 CR001129 58 − CUCUGAUUAGGGUGGGGGCG Chr2: 60495244-60495266 339 CR001130 58 − GAUUAGGGUGGGGGCGUGGG Chr2: 60495249-60495271 340 CR001131 58 − AUUAGGGUGGGGGCGUGGGU Chr2: 60495250-60495272 341

In some aspects of the invention, it is preferred that the gRNA molecule to the +58 Enhancer region of BCL11a comprise a targeting domain of a gRNA listed in FIG. 11. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 341. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 246. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 248. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 247. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 245. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 249. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 244. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 199. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 251. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 250. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 334. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 185. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 186. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 336. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 337.

In some aspects of the invention, e.g., as indicated herein, it may be beneficial to include gRNA moleucles targeting more than one, e.g., two, target sites (e.g., a first gRNA molecule and a second gRNA molecule). In some embodiments, the two target sites are both located in the +58 BCL11a enhancer region. In such aspects, any combination of more than one, e.g., two, gRNA molecules (e.g., a first gRNA molecule and a second gRNA molecule) comprising targeting domains listed in Table 7 may be used. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 246, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 248, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 247, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 245, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 249, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 341 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 248, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 247, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 245, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 249, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 246 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 246, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 247, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 245, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 249, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 248 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 246, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 248, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 245, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 249, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 247 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 246, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 248, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 247, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 249, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 245 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 246, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 248, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 247, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 245, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 249 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 246, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 248, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 247, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 245, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 249, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 244 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 246, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 248, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 247, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 245, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 249, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 199 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 246, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 248, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 247, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 245, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 249, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 251 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 246, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 248, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 247, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 245, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 249, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 250 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 246, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 248, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 247, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 245, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 249, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 334 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 246, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 248, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 247, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 245, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 249, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 185 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 246, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 248, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 247, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 245, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 249, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 186 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 246, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 248, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 247, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 245, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 249, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 336 and SEQ ID NO: 337, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 336, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 246, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 248, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 247, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 245, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 249, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 244, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 199, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 251, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 250, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 334, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 185, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 186, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 337 and SEQ ID NO: 336, respectively.

In embodiments, the aspects of the invention relate to or incorporate a gRNA molecule that is complementary to a target sequence within the +58 enhancer region of the BCL11a gene which is disposed 3′ to the GATA-1 binding site, e.g., 3′ to the GATA1 binding site and TAL-1 binding site. In embodiments, the CRISPR system comprising a gRNA molecule described herein induces one or more indels at or near the target site. In embodiments, the indel does not comprise a nucleotide of a GATA-1 binding site and/or does not comprise a nucleotide of a TAL-1 binding site. In embodiments, the CRISPR system induces one or more frameshift indels at or near the target site, e.g., at an overall frameshift indel rate of at least about 10%, at least about 20%, at least about 30%, at least about 40%, or at least about 50%, e.g., as measured by NGS. In embodiments, the overall indel rate is at least about 70%, at least about 80%, at least about 90%, or at least about 95%, e.g., as measured by NGS.

TABLE 8 Preferred Guide RNA Targeting Domains directed to the +62 Enhancer Region of the BCL11a Gene (i.e., to a BCL11a Enhancer) Exon/ SEQ ID Id. Feature Strand Targeting domain Locations NO: CR00171 62 − AGCUCUGGAAUGAUGGCUUA Chr2: 60490354-60490376 278 CR00172 62 − AUUGUGGAGCUCUGGAAUGA Chr2: 60490361-60490383 279 CR00173 62 − CUGGAAUAGAAAAUUGGAGU Chr2: 60490384-60490406 280 CR00174 62 − UGGGUACGGGGAACUAAGAC Chr2: 60490403-60490425 281 CR00175 62 + UUAGUUCCCCGUACCCAUCA Chr2: 60490409-60490431 282 CR00176 62 − UAUUUUCCUUGAUGGGUACG Chr2: 60490415-60490437 283 CR00177 62 − AUAUUUUCCUUGAUGGGUAC Chr2: 60490416-60490438 284 CR00178 62 − AAUAUUUUCCUUGAUGGGUA Chr2: 60490417-60490439 285 CR00179 62 − GGAAGGAAAUGAGAACGGAA Chr2: 60490456-60490478 286 CR00180 62 − AGGAAGGAAAUGAGAACGGA Chr2: 60490457-60490479 287 CR00181 62 + AUACUUCAAGGCCUCAAUGA Chr2: 60490520-60490542 288 CR00182 62 − GACUAGGUAGACCUUCAUUG Chr2: 60490531-60490553 289 CR00183 62 − UUCUUCUUGCUAAGGUGACU Chr2: 60490547-60490569 290 CR00184 62 − GAGAUUGAUUCUUCUUGCUA Chr2: 60490555-60490577 291 CR00185 62 − GUGUUCUAUGAGGUUGGAGA Chr2: 60490580-60490602 292 CR00186 62 − GGAUGAGUGUUCUAUGAGGU Chr2: 60490586-60490608 293 CR00187 62 − CAUGGGAUGAGUGUUCUAUG Chr2: 60490590-60490612 294 CR00188 62 − UGAGUCAGGGAGUGGUGCAU Chr2: 60490607-60490629 295 CR00189 62 − AUGAGUCAGGGAGUGGUGCA Chr2: 60490608-60490630 296 CR00190 62 + CCACUCCCUGACUCAUAUCU Chr2: 60490615-60490637 297 CR00191 62 − UAAGGCCUAGAUAUGAGUCA Chr2: 60490620-60490642 298 CR00192 62 − GUAAGGCCUAGAUAUGAGUC Chr2: 60490621-60490643 299 CR00193 62 + AUAUCUAGGCCUUACAUUGC Chr2: 60490629-60490651 300 CR00194 62 − AAAUUAAUUAGAGGCAUAGA Chr2: 60490656-60490678 301 CR00195 62 − GAAAUUAAUUAGAGGCAUAG Chr2: 60490657-60490679 302 CR00196 62 − GAACACAUGAAAUUAAUUAG Chr2: 60490665-60490687 303 CR00197 62 + CCAAUGAGUUUCUUCAAUAC Chr2: 60490688-60490710 304 CR00198 62 − CAAAUAUAAUAGAAGCAAGU Chr2: 60490721-60490743 305 CR00199 62 − AAAUAACUUCCCUUUUAGGA Chr2: 60490821-60490843 306 CR00200 62 − GGAAAAAUAACUUCCCUUUU Chr2: 60490825-60490847 307 CR00201 62 − UUUUGAACAGAAAUGAUAUU Chr2: 60490846-60490868 308 CR00202 62 − AGUUCAAGUAGAUAUCAGAA Chr2: 60490905-60490927 309 CR00203 62 − AAGUUCAAGUAGAUAUCAGA Chr2: 60490906-60490928 310 CR00204 62 − GGGUGGCUGUUUAAAGAGGG Chr2: 60490994-60491016 311 CR00205 62 − GUGGGGUGGCUGUUUAAAGA Chr2: 60490997-60491019 312 CR00206 62 − UGUGGGGUGGCUGUUUAAAG Chr2: 60490998-60491020 313 CR00207 62 + UGCCAACCAGACUGUGCGCC Chr2: 60491051-60491073 314 CR00208 62 − AACCUGGCGCACAGUCUGGU Chr2: 60491053-60491075 315 CR00209 62 + AACCAGACUGUGCGCCAGGU Chr2: 60491055-60491077 316 CR00210 62 − UACCAACCUGGCGCACAGUC Chr2: 60491057-60491079 317 CR00211 62 − UCUGUCAGACUUUACCAACC Chr2: 60491069-60491091 318 CR00212 62 + AUAUGUGAAGCCCAACUACG Chr2: 60491118-60491140 319 CR00213 62 − AGUUGCACAACCACGUAGUU Chr2: 60491128-60491150 320 CR00214 62 − GAGUUGCACAACCACGUAGU Chr2: 60491129-60491151 321 CR00215 62 + CUAUAGCUGACUUUCAACCA Chr2: 60491151-60491173 322 CR00216 62 − AACUUCUUUGCAGAUGACCA Chr2: 60491168-60491190 323 CR00217 62 − UUGCAUUGAGGAUGCGCAGG Chr2: 60491199-60491221 324 CR00218 62 − UUUUUGCAUUGAGGAUGCGC Chr2: 60491202-60491224 325 CR00221 62 + GACCUCAUUUUGAUGCCAGA Chr2: 60491281-60491303 326 CR00222 62 − UGCCCUCUGGCAUCAAAAUG Chr2: 60491283-60491305 327 CR00223 62 + AUGCCAGAGGGCAGCAAACA Chr2: 60491293-60491315 328 CR00224 62 − CUGUACUUAAUAGCUGAAGG Chr2: 60491326-60491348 329 CR00225 62 − ACUGUACUUAAUAGCUGAAG Chr2: 60491327-60491349 330 CR00227 62 + CAGCUAUUAAGUACAGUAAA Chr2: 60491333-60491355 331 CR00228 62 − GAGCAUUUCAAAUGAUAGUU Chr2: 60491360-60491382 332 CR00229 62 + CAUUUGAAAUGCUCCCGGCC Chr2: 60491369-60491391 333

In some aspects of the invention, it is preferred that the gRNA molecule to the +62 Enhancer region of BCL11a comprise a targeting domain of a gRNA listed in FIG. 12. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 318. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 312. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 313. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 294. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 310. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 319. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 298. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 322. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 311. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 315. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 290. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 317. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 309. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 289. In an aspect, the gRNA molecule includes a targeting domain comprising, e.g., consisting of, SEQ ID NO: 281.

In some aspects of the invention, e.g., as indicated herein, it may be beneficial to include gRNA moleucles targeting more than one, e.g., two, target sites (e.g., a first gRNA molecule and a second gRNA molecule). In some embodiments, the two target sites are both located in the +62 BCL11a enhancer region. In such aspects, any combination of more than one, e.g., two, gRNA molecules (e.g., a first gRNA molecule and a second gRNA molecule) comprising targeting domains listed in Table 8 may be used. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 318 and SEQ ID NO: 312, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 318 and SEQ ID NO: 313, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 318 and SEQ ID NO: 294, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 318 and SEQ ID NO: 310, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 318 and SEQ ID NO: 319, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 318 and SEQ ID NO: 298, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 318 and SEQ ID NO: 322, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 318 and SEQ ID NO: 311, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 318 and SEQ ID NO: 315, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 318 and SEQ ID NO: 290, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 318 and SEQ ID NO: 317, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 318 and SEQ ID NO: 309, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 318 and SEQ ID NO: 289, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 318 and SEQ ID NO: 281, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 312 and SEQ ID NO: 313, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 312 and SEQ ID NO: 294, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 312 and SEQ ID NO: 310, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 312 and SEQ ID NO: 319, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 312 and SEQ ID NO: 298, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 312 and SEQ ID NO: 322, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 312 and SEQ ID NO: 311, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 312 and SEQ ID NO: 315, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 312 and SEQ ID NO: 290, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 312 and SEQ ID NO: 317, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 312 and SEQ ID NO: 309, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 312 and SEQ ID NO: 289, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 312 and SEQ ID NO: 281, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 313 and SEQ ID NO: 312, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 313 and SEQ ID NO: 294, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 313 and SEQ ID NO: 310, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 313 and SEQ ID NO: 319, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 313 and SEQ ID NO: 298, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 313 and SEQ ID NO: 322, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 313 and SEQ ID NO: 311, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 313 and SEQ ID NO: 315, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 313 and SEQ ID NO: 290, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 313 and SEQ ID NO: 317, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 313 and SEQ ID NO: 309, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 313 and SEQ ID NO: 289, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 313 and SEQ ID NO: 281, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 294 and SEQ ID NO: 312, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 294 and SEQ ID NO: 313, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 294 and SEQ ID NO: 310, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 294 and SEQ ID NO: 319, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 294 and SEQ ID NO: 298, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 294 and SEQ ID NO: 322, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 294 and SEQ ID NO: 311, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 294 and SEQ ID NO: 315, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 294 and SEQ ID NO: 290, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 294 and SEQ ID NO: 317, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 294 and SEQ ID NO: 309, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 294 and SEQ ID NO: 289, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 294 and SEQ ID NO: 281, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 310 and SEQ ID NO: 312, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 310 and SEQ ID NO: 313, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 310 and SEQ ID NO: 294, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 310 and SEQ ID NO: 319, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 310 and SEQ ID NO: 298, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 310 and SEQ ID NO: 322, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 310 and SEQ ID NO: 311, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 310 and SEQ ID NO: 315, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 310 and SEQ ID NO: 290, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 310 and SEQ ID NO: 317, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 310 and SEQ ID NO: 309, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 310 and SEQ ID NO: 289, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 310 and SEQ ID NO: 281, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 319 and SEQ ID NO: 312, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 319 and SEQ ID NO: 313, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 319 and SEQ ID NO: 294, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 319 and SEQ ID NO: 310, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 319 and SEQ ID NO: 298, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 319 and SEQ ID NO: 322, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 319 and SEQ ID NO: 311, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 319 and SEQ ID NO: 315, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 319 and SEQ ID NO: 290, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 319 and SEQ ID NO: 317, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 319 and SEQ ID NO: 309, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 319 and SEQ ID NO: 289, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 319 and SEQ ID NO: 281, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 298 and SEQ ID NO: 312, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 298 and SEQ ID NO: 313, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 298 and SEQ ID NO: 294, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 298 and SEQ ID NO: 310, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 298 and SEQ ID NO: 319, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 298 and SEQ ID NO: 322, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 298 and SEQ ID NO: 311, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 298 and SEQ ID NO: 315, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 298 and SEQ ID NO: 290, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 298 and SEQ ID NO: 317, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 298 and SEQ ID NO: 309, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 298 and SEQ ID NO: 289, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 298 and SEQ ID NO: 281, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 322 and SEQ ID NO: 312, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 322 and SEQ ID NO: 313, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 322 and SEQ ID NO: 294, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 322 and SEQ ID NO: 310, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 322 and SEQ ID NO: 319, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 322 and SEQ ID NO: 298, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 322 and SEQ ID NO: 311, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 322 and SEQ ID NO: 315, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 322 and SEQ ID NO: 290, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 322 and SEQ ID NO: 317, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 322 and SEQ ID NO: 309, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 322 and SEQ ID NO: 289, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 322 and SEQ ID NO: 281, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 311 and SEQ ID NO: 312, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 311 and SEQ ID NO: 313, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 311 and SEQ ID NO: 294, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 311 and SEQ ID NO: 310, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 311 and SEQ ID NO: 319, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 311 and SEQ ID NO: 298, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 311 and SEQ ID NO: 322, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 311 and SEQ ID NO: 315, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 311 and SEQ ID NO: 290, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 311 and SEQ ID NO: 317, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 311 and SEQ ID NO: 309, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 311 and SEQ ID NO: 289, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 311 and SEQ ID NO: 281, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 315 and SEQ ID NO: 312, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 315 and SEQ ID NO: 313, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 315 and SEQ ID NO: 294, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 315 and SEQ ID NO: 310, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 315 and SEQ ID NO: 319, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 315 and SEQ ID NO: 298, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 315 and SEQ ID NO: 322, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 315 and SEQ ID NO: 311, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 315 and SEQ ID NO: 290, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 315 and SEQ ID NO: 317, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 315 and SEQ ID NO: 309, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 315 and SEQ ID NO: 289, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 315 and SEQ ID NO: 281, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 290 and SEQ ID NO: 312, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 290 and SEQ ID NO: 313, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 290 and SEQ ID NO: 294, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 290 and SEQ ID NO: 310, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 290 and SEQ ID NO: 319, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 290 and SEQ ID NO: 298, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 290 and SEQ ID NO: 322, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 290 and SEQ ID NO: 311, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 290 and SEQ ID NO: 315, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 290 and SEQ ID NO: 317, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 290 and SEQ ID NO: 309, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 290 and SEQ ID NO: 289, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 290 and SEQ ID NO: 281, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 317 and SEQ ID NO: 312, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 317 and SEQ ID NO: 313, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 317 and SEQ ID NO: 294, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 317 and SEQ ID NO: 310, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 317 and SEQ ID NO: 319, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 317 and SEQ ID NO: 298, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 317 and SEQ ID NO: 322, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 317 and SEQ ID NO: 311, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 317 and SEQ ID NO: 315, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 317 and SEQ ID NO: 290, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 317 and SEQ ID NO: 309, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 317 and SEQ ID NO: 289, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 317 and SEQ ID NO: 281, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 309 and SEQ ID NO: 312, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 309 and SEQ ID NO: 313, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 309 and SEQ ID NO: 294, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 309 and SEQ ID NO: 310, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 309 and SEQ ID NO: 319, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 309 and SEQ ID NO: 298, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 309 and SEQ ID NO: 322, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 309 and SEQ ID NO: 311, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 309 and SEQ ID NO: 315, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 309 and SEQ ID NO: 290, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 309 and SEQ ID NO: 317, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 309 and SEQ ID NO: 289, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 309 and SEQ ID NO: 281, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 289 and SEQ ID NO: 312, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 289 and SEQ ID NO: 313, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 289 and SEQ ID NO: 294, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 289 and SEQ ID NO: 310, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 289 and SEQ ID NO: 319, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 289 and SEQ ID NO: 298, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 289 and SEQ ID NO: 322, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 289 and SEQ ID NO: 311, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 289 and SEQ ID NO: 315, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 289 and SEQ ID NO: 290, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 289 and SEQ ID NO: 317, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 289 and SEQ ID NO: 309, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 289 and SEQ ID NO: 281, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 281 and SEQ ID NO: 312, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 281 and SEQ ID NO: 313, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 281 and SEQ ID NO: 294, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 281 and SEQ ID NO: 310, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 281 and SEQ ID NO: 319, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 281 and SEQ ID NO: 298, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 281 and SEQ ID NO: 322, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 281 and SEQ ID NO: 311, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 281 and SEQ ID NO: 315, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 281 and SEQ ID NO: 290, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 281 and SEQ ID NO: 317, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 281 and SEQ ID NO: 309, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 281 and SEQ ID NO: 289, respectively.

TABLE 9 Preferred Guide RNA Targeting Domains directed to the +55 Enhancer Region of the BCL11a Gene (i.e., to a BCL11a Enhancer) SEQ ID ID Species Strand Location Targeting Domain Sequence NO: CR002142 h + Chr2: 60498031-60498053 CCUGGCAGACCCUCAAGAGC 1596 CR002143 h − Chr2: 60498031-60498053 CCUGGCAGACCCUCAAGAGC 1597 CR002144 h + Chr2: 60498032-60498054 CUGGCAGACCCUCAAGAGCA 1598 CR002145 h + Chr2: 60498033-60498055 UGGCAGACCCUCAAGAGCAG 1599 CR002146 h − Chr2: 60498040-60498062 CCCUCAAGAGCAGGGGUCUU 1600 CR002147 h − Chr2: 60498041-60498063 CCUCAAGAGCAGGGGUCUUC 1601 CR001262 h + Chr1: 55039155-55039177 UAAGGCCAGUGGAAAGAAUU 1602 CR002148 h + Chr2: 60498045-60498067 AAGAGCAGGGGUCUUCUCUU 1603 CR002149 h + Chr2: 60498046-60498068 AGAGCAGGGGUCUUCUCUUU 1604 CR002150 h + Chr2: 60498047-60498069 GAGCAGGGGUCUUCUCUUUG 1605 CR002151 h + Chr2: 60498048-60498070 AGCAGGGGUCUUCUCUUUGG 1606 CR002152 h + Chr2: 60498051-60498073 AGGGGUCUUCUCUUUGGGGG 1607 CR002153 h + Chr2: 60498068-60498090 GGGAGGACAUCACUCUUAGC 1608 CR002154 h + Chr2: 60498069-60498091 GGAGGACAUCACUCUUAGCA 1609 CR001261 h − Chr1: 55039269-55039291 GCCAGACUCCAAGUUCUGCC 1610 CR002155 h + Chr2: 60498073-60498095 GACAUCACUCUUAGCAGGGC 1611 CR002156 h + Chr2: 60498074-60498096 ACAUCACUCUUAGCAGGGCU 1612 CR002157 h + Chr2: 60498075-60498097 CAUCACUCUUAGCAGGGCUG 1613 CR002158 h + Chr2: 60498091-60498113 GCUGGGGUGAGUCAAAAGUC 1614 CR002159 h + Chr2: 60498092-60498114 CUGGGGUGAGUCAAAAGUCU 1615 CR002160 h + Chr2: 60498099-60498121 GAGUCAAAAGUCUGGGAGAA 1616 CR002161 h + Chr2: 60498102-60498124 UCAAAAGUCUGGGAGAAUGG 1617 CR002162 h + Chr2: 60498107-60498129 AGUCUGGGAGAAUGGAGGUG 1618 CR002163 h + Chr2: 60498110-60498132 CUGGGAGAAUGGAGGUGUGG 1619 CR002164 h + Chr2: 60498111-60498133 UGGGAGAAUGGAGGUGUGGA 1620 CR002165 h + Chr2: 60498112-60498134 GGGAGAAUGGAGGUGUGGAG 1621 CR002166 h + Chr2: 60498120-60498142 GGAGGUGUGGAGGGGAUAAC 1622 CR001263 h + Chr1: 55039180-55039202 GGCAGCGAGGAGUCCACAGU 1623 CR002167 h + Chr2: 60498121-60498143 GAGGUGUGGAGGGGAUAACU 1624 CR002168 h + Chr2: 60498137-60498159 AACUGGGUCAGACCCCAAGC 1625 CR002169 h + Chr2: 60498141-60498163 GGGUCAGACCCCAAGCAGGA 1626 CR002170 h + Chr2: 60498142-60498164 GGUCAGACCCCAAGCAGGAA 1627 CR002171 h − Chr2: 60498149-60498171 CCCCAAGCAGGAAGGGCCUC 1628 CR002172 h − Chr2: 60498150-60498172 CCCAAGCAGGAAGGGCCUCU 1629 CR002173 h − Chr2: 60498151-60498173 CCAAGCAGGAAGGGCCUCUA 1630 CR002174 h + Chr2: 60498157-60498179 AGGAAGGGCCUCUAUGUAGA 1631 CR002175 h + Chr2: 60498158-60498180 GGAAGGGCCUCUAUGUAGAC 1632 CR002176 h + Chr2: 60498165-60498187 CCUCUAUGUAGACGGGUGUG 1633 CR002177 h − Chr2: 60498165-60498187 CCUCUAUGUAGACGGGUGUG 1634 CR002178 h + Chr2: 60498175-60498197 GACGGGUGUGUGGCUCCUUA 1635 CR002179 h − Chr2: 60498190-60498212 CCUUAAGGUGACCCAGCAGC 1636 CR002180 h + Chr2: 60498192-60498214 UUAAGGUGACCCAGCAGCCC 1637 CR002181 h + Chr2: 60498193-60498215 UAAGGUGACCCAGCAGCCCU 1638 CR002182 h − Chr2: 60498201-60498223 CCCAGCAGCCCUGGGCACAG 1639 CR002183 h − Chr2: 60498202-60498224 CCAGCAGCCCUGGGCACAGA 1640 CR001261 h − Chr1: 55039269-55039291 GCCAGACUCCAAGUUCUGCC 1641 CR002184 h + Chr2: 60498204-60498226 AGCAGCCCUGGGCACAGAAG 1642 CR002185 h − Chr2: 60498209-60498231 CCCUGGGCACAGAAGUGGUG 1643 CR002186 h − Chr2: 60498210-60498232 CCUGGGCACAGAAGUGGUGC 1644 CR002187 h + Chr2: 60498211-60498233 CUGGGCACAGAAGUGGUGCG 1645 CR002188 h + Chr2: 60498240-60498262 UGCCAACAGUGAUAACCAGC 1646 CR002189 h + Chr2: 60498241-60498263 GCCAACAGUGAUAACCAGCA 1647 CR001262 h + Chr1: 55039155-55039177 UAAGGCCAGUGGAAAGAAUU 1648 CR002190 h − Chr2: 60498242-60498264 CCAACAGUGAUAACCAGCAG 1649 CR002191 h + Chr2: 60498255-60498277 CCAGCAGGGCCUGUCAGAAG 1650 CR002192 h − Chr2: 60498255-60498277 CCAGCAGGGCCUGUCAGAAG 1651 CR002193 h + Chr2: 60498261-60498283 GGGCCUGUCAGAAGAGGCCC 1652 CR002194 h − Chr2: 60498264-60498286 CCUGUCAGAAGAGGCCCUGG 1653 CR002195 h + Chr2: 60498271-60498293 GAAGAGGCCCUGGACACUGA 1654 CR002196 h + Chr2: 60498275-60498297 AGGCCCUGGACACUGAAGGC 1655 CR002197 h + Chr2: 60498276-60498298 GGCCCUGGACACUGAAGGCU 1656 CR001264 h − Chr1: 55039149-55039171 UCUUUCCACUGGCCUUAACC 1657 CR002198 h − Chr2: 60498278-60498300 CCCUGGACACUGAAGGCUGG 1658 CR002199 h − Chr2: 60498279-60498301 CCUGGACACUGAAGGCUGGG 1659 CR002200 h + Chr2: 60498287-60498309 CUGAAGGCUGGGCACAGCCU 1660 CR002201 h + Chr2: 60498288-60498310 UGAAGGCUGGGCACAGCCUU 1661 CR002202 h + Chr2: 60498289-60498311 GAAGGCUGGGCACAGCCUUG 1662 CR002203 h + Chr2: 60498301-60498323 CAGCCUUGGGGACCGCUCAC 1663 CR002204 h − Chr2: 60498304-60498326 CCUUGGGGACCGCUCACAGG 1664 CR002205 h − Chr2: 60498313-60498335 CCGCUCACAGGACAUGCAGC 1665 CR002206 h − Chr2: 60498341-60498363 CCGACAACUCCCUACCGCGA 1666 CR002207 h − Chr2: 60498350-60498372 CCCUACCGCGACCCCUAUCA 1667 CR002208 h − Chr2: 60498351-60498373 CCUACCGCGACCCCUAUCAG 1668 CR002209 h − Chr2: 60498355-60498377 CCGCGACCCCUAUCAGUGCC 1669 CR002210 h − Chr2: 60498361-60498383 CCCCUAUCAGUGCCGACCAA 1670 CR002211 h − Chr2: 60498362-60498384 CCCUAUCAGUGCCGACCAAG 1671 CR002212 h − Chr2: 60498363-60498385 CCUAUCAGUGCCGACCAAGC 1672 CR002213 h − Chr2: 60498373-60498395 CCGACCAAGCACACAAGAUG 1673 CR002214 h − Chr2: 60498377-60498399 CCAAGCACACAAGAUGCACA 1674 CR002215 h + Chr2: 60498380-60498402 AGCACACAAGAUGCACACCC 1675 CR002216 h + Chr2: 60498384-60498406 CACAAGAUGCACACCCAGGC 1676 CR002217 h + Chr2: 60498385-60498407 ACAAGAUGCACACCCAGGCU 1677 CR001264 h − Chr1: 55039149-55039171 UCUUUCCACUGGCCUUAACC 1678 CR002218 h + Chr2: 60498389-60498411 GAUGCACACCCAGGCUGGGC 1679 CR002219 h + Chr2: 60498396-60498418 ACCCAGGCUGGGCUGGACAG 1680 CR002220 h + Chr2: 60498397-60498419 CCCAGGCUGGGCUGGACAGA 1681 CR002221 h − Chr2: 60498397-60498419 CCCAGGCUGGGCUGGACAGA 1682 CR002222 h + Chr2: 60498398-60498420 CCAGGCUGGGCUGGACAGAG 1683 CR002223 h − Chr2: 60498398-60498420 CCAGGCUGGGCUGGACAGAG 1684 CR002224 h + Chr2: 60498415-60498437 GAGGGGUCCCACAAGAUCAC 1685 CR002225 h + Chr2: 60498416-60498438 AGGGGUCCCACAAGAUCACA 1686 CR002226 h − Chr2: 60498422-60498444 CCCACAAGAUCACAGGGUGU 1687 CR001263 h + Chr1: 55039180-55039202 GGCAGCGAGGAGUCCACAGU 1688 CR002227 h − Chr2: 60498423-60498445 CCACAAGAUCACAGGGUGUG 1689 CR002228 h + Chr2: 60498431-60498453 UCACAGGGUGUGCCCUGAGA 1690 CR002229 h + Chr2: 60498434-60498456 CAGGGUGUGCCCUGAGAAGG 1691

In some aspects of the invention, it is preferred that the gRNA molecule to the +55 Enhancer region of BCL11a comprise a targeting domain comprising, e.g., consisting of a targeting domain sequence selected from SEQ ID NO: 1683, SEQ ID NO: 1638, SEQ ID NO: 1647, SEQ ID NO: 1609, SEQ ID NO: 1621, SEQ ID NO: 1617, SEQ ID NO: 1654, SEQ ID NO: 1631, SEQ ID NO: 1620, SEQ ID NO: 1637, SEQ ID NO: 1612, SEQ ID NO: 1656, SEQ ID NO: 1619, SEQ ID NO: 1675, SEQ ID NO: 1645, SEQ ID NO: 1598, SEQ ID NO: 1599, SEQ ID NO: 1663, SEQ ID NO: 1677, and SEQ ID NO: 1626.

In some aspects of the invention, e.g., as indicated herein, it may be beneficial to include gRNA moleucles targeting more than one, e.g., two, target sites (e.g., a first gRNA molecule and a second gRNA molecule). In some embodiments, the two target sites are both located in the +55 BCL11a enhancer region. In such aspects, any combination of more than one, e.g., two, gRNA molecules (e.g., a first gRNA molecule and a second gRNA molecule) comprising, e.g., consisting of, targeting domains listed in Table 9 may be used, that target different target sites of the +55 BCL11a enhancer region. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1683 and SEQ ID NO: 1638, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1683 and SEQ ID NO: 1647, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1683 and SEQ ID NO: 1609, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1683 and SEQ ID NO: 1621, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1683 and SEQ ID NO: 1617, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1683 and SEQ ID NO: 1654, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1683 and SEQ ID NO: 1631, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1683 and SEQ ID NO: 1620, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1683 and SEQ ID NO: 1637, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1683 and SEQ ID NO: 1612, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1683 and SEQ ID NO: 1656, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1683 and SEQ ID NO: 1619, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1683 and SEQ ID NO: 1675, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1683 and SEQ ID NO: 1645, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1683 and SEQ ID NO: 1598, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1683 and SEQ ID NO: 1599, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1683 and SEQ ID NO: 1663, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1683 and SEQ ID NO: 1677, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1683 and SEQ ID NO: 1626, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1638 and SEQ ID NO: 1647, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1638 and SEQ ID NO: 1609, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1638 and SEQ ID NO: 1621, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1638 and SEQ ID NO: 1617, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1638 and SEQ ID NO: 1654, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1638 and SEQ ID NO: 1631, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1638 and SEQ ID NO: 1620, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1638 and SEQ ID NO: 1637, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1638 and SEQ ID NO: 1612, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1638 and SEQ ID NO: 1656, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1638 and SEQ ID NO: 1619, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1638 and SEQ ID NO: 1675, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1638 and SEQ ID NO: 1645, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1638 and SEQ ID NO: 1598, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1638 and SEQ ID NO: 1599, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1638 and SEQ ID NO: 1663, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1638 and SEQ ID NO: 1677, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1638 and SEQ ID NO: 1626, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1647 and SEQ ID NO: 1638, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1647 and SEQ ID NO: 1609, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1647 and SEQ ID NO: 1621, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1647 and SEQ ID NO: 1617, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1647 and SEQ ID NO: 1654, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1647 and SEQ ID NO: 1631, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1647 and SEQ ID NO: 1620, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1647 and SEQ ID NO: 1637, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1647 and SEQ ID NO: 1612, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1647 and SEQ ID NO: 1656, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1647 and SEQ ID NO: 1619, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1647 and SEQ ID NO: 1675, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1647 and SEQ ID NO: 1645, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1647 and SEQ ID NO: 1598, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1647 and SEQ ID NO: 1599, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1647 and SEQ ID NO: 1663, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1647 and SEQ ID NO: 1677, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1647 and SEQ ID NO: 1626, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1609 and SEQ ID NO: 1638, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1609 and SEQ ID NO: 1647, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1609 and SEQ ID NO: 1621, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1609 and SEQ ID NO: 1617, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1609 and SEQ ID NO: 1654, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1609 and SEQ ID NO: 1631, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1609 and SEQ ID NO: 1620, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1609 and SEQ ID NO: 1637, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1609 and SEQ ID NO: 1612, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1609 and SEQ ID NO: 1656, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1609 and SEQ ID NO: 1619, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1609 and SEQ ID NO: 1675, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1609 and SEQ ID NO: 1645, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1609 and SEQ ID NO: 1598, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1609 and SEQ ID NO: 1599, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1609 and SEQ ID NO: 1663, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1609 and SEQ ID NO: 1677, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1609 and SEQ ID NO: 1626, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1621 and SEQ ID NO: 1638, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1621 and SEQ ID NO: 1647, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1621 and SEQ ID NO: 1609, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1621 and SEQ ID NO: 1617, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1621 and SEQ ID NO: 1654, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1621 and SEQ ID NO: 1631, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1621 and SEQ ID NO: 1620, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1621 and SEQ ID NO: 1637, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1621 and SEQ ID NO: 1612, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1621 and SEQ ID NO: 1656, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1621 and SEQ ID NO: 1619, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1621 and SEQ ID NO: 1675, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1621 and SEQ ID NO: 1645, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1621 and SEQ ID NO: 1598, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1621 and SEQ ID NO: 1599, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1621 and SEQ ID NO: 1663, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1621 and SEQ ID NO: 1677, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1621 and SEQ ID NO: 1626, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1617 and SEQ ID NO: 1638, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1617 and SEQ ID NO: 1647, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1617 and SEQ ID NO: 1609, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1617 and SEQ ID NO: 1621, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1617 and SEQ ID NO: 1654, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1617 and SEQ ID NO: 1631, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1617 and SEQ ID NO: 1620, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1617 and SEQ ID NO: 1637, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1617 and SEQ ID NO: 1612, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1617 and SEQ ID NO: 1656, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1617 and SEQ ID NO: 1619, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1617 and SEQ ID NO: 1675, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1617 and SEQ ID NO: 1645, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1617 and SEQ ID NO: 1598, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1617 and SEQ ID NO: 1599, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1617 and SEQ ID NO: 1663, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1617 and SEQ ID NO: 1677, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1617 and SEQ ID NO: 1626, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1654 and SEQ ID NO: 1638, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1654 and SEQ ID NO: 1647, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1654 and SEQ ID NO: 1609, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1654 and SEQ ID NO: 1621, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1654 and SEQ ID NO: 1617, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1654 and SEQ ID NO: 1631, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1654 and SEQ ID NO: 1620, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1654 and SEQ ID NO: 1637, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1654 and SEQ ID NO: 1612, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1654 and SEQ ID NO: 1656, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1654 and SEQ ID NO: 1619, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1654 and SEQ ID NO: 1675, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1654 and SEQ ID NO: 1645, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1654 and SEQ ID NO: 1598, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1654 and SEQ ID NO: 1599, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1654 and SEQ ID NO: 1663, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1654 and SEQ ID NO: 1677, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1654 and SEQ ID NO: 1626, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1631 and SEQ ID NO: 1638, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1631 and SEQ ID NO: 1647, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1631 and SEQ ID NO: 1609, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1631 and SEQ ID NO: 1621, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1631 and SEQ ID NO: 1617, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1631 and SEQ ID NO: 1654, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1631 and SEQ ID NO: 1620, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1631 and SEQ ID NO: 1637, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1631 and SEQ ID NO: 1612, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1631 and SEQ ID NO: 1656, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1631 and SEQ ID NO: 1619, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1631 and SEQ ID NO: 1675, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1631 and SEQ ID NO: 1645, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1631 and SEQ ID NO: 1598, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1631 and SEQ ID NO: 1599, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1631 and SEQ ID NO: 1663, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1631 and SEQ ID NO: 1677, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1631 and SEQ ID NO: 1626, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1620 and SEQ ID NO: 1638, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1620 and SEQ ID NO: 1647, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1620 and SEQ ID NO: 1609, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1620 and SEQ ID NO: 1621, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1620 and SEQ ID NO: 1617, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1620 and SEQ ID NO: 1654, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1620 and SEQ ID NO: 1631, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1620 and SEQ ID NO: 1637, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1620 and SEQ ID NO: 1612, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1620 and SEQ ID NO: 1656, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1620 and SEQ ID NO: 1619, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1620 and SEQ ID NO: 1675, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1620 and SEQ ID NO: 1645, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1620 and SEQ ID NO: 1598, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1620 and SEQ ID NO: 1599, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1620 and SEQ ID NO: 1663, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1620 and SEQ ID NO: 1677, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1620 and SEQ ID NO: 1626, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1637 and SEQ ID NO: 1638, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1637 and SEQ ID NO: 1647, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1637 and SEQ ID NO: 1609, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1637 and SEQ ID NO: 1621, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1637 and SEQ ID NO: 1617, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1637 and SEQ ID NO: 1654, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1637 and SEQ ID NO: 1631, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1637 and SEQ ID NO: 1620, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1637 and SEQ ID NO: 1612, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1637 and SEQ ID NO: 1656, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1637 and SEQ ID NO: 1619, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1637 and SEQ ID NO: 1675, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1637 and SEQ ID NO: 1645, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1637 and SEQ ID NO: 1598, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1637 and SEQ ID NO: 1599, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1637 and SEQ ID NO: 1663, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1637 and SEQ ID NO: 1677, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1637 and SEQ ID NO: 1626, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1612 and SEQ ID NO: 1638, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1612 and SEQ ID NO: 1647, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1612 and SEQ ID NO: 1609, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1612 and SEQ ID NO: 1621, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1612 and SEQ ID NO: 1617, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1612 and SEQ ID NO: 1654, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1612 and SEQ ID NO: 1631, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1612 and SEQ ID NO: 1620, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1612 and SEQ ID NO: 1637, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1612 and SEQ ID NO: 1656, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1612 and SEQ ID NO: 1619, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1612 and SEQ ID NO: 1675, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1612 and SEQ ID NO: 1645, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1612 and SEQ ID NO: 1598, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1612 and SEQ ID NO: 1599, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1612 and SEQ ID NO: 1663, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1612 and SEQ ID NO: 1677, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1612 and SEQ ID NO: 1626, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1656 and SEQ ID NO: 1638, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1656 and SEQ ID NO: 1647, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1656 and SEQ ID NO: 1609, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1656 and SEQ ID NO: 1621, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1656 and SEQ ID NO: 1617, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1656 and SEQ ID NO: 1654, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1656 and SEQ ID NO: 1631, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1656 and SEQ ID NO: 1620, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1656 and SEQ ID NO: 1637, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1656 and SEQ ID NO: 1612, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1656 and SEQ ID NO: 1619, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1656 and SEQ ID NO: 1675, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1656 and SEQ ID NO: 1645, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1656 and SEQ ID NO: 1598, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1656 and SEQ ID NO: 1599, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1656 and SEQ ID NO: 1663, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1656 and SEQ ID NO: 1677, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1656 and SEQ ID NO: 1626, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1619 and SEQ ID NO: 1638, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1619 and SEQ ID NO: 1647, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1619 and SEQ ID NO: 1609, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1619 and SEQ ID NO: 1621, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1619 and SEQ ID NO: 1617, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1619 and SEQ ID NO: 1654, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1619 and SEQ ID NO: 1631, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1619 and SEQ ID NO: 1620, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1619 and SEQ ID NO: 1637, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1619 and SEQ ID NO: 1612, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1619 and SEQ ID NO: 1656, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1619 and SEQ ID NO: 1675, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1619 and SEQ ID NO: 1645, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1619 and SEQ ID NO: 1598, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1619 and SEQ ID NO: 1599, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1619 and SEQ ID NO: 1663, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1619 and SEQ ID NO: 1677, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1619 and SEQ ID NO: 1626, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1675 and SEQ ID NO: 1638, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1675 and SEQ ID NO: 1647, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1675 and SEQ ID NO: 1609, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1675 and SEQ ID NO: 1621, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1675 and SEQ ID NO: 1617, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1675 and SEQ ID NO: 1654, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1675 and SEQ ID NO: 1631, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1675 and SEQ ID NO: 1620, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1675 and SEQ ID NO: 1637, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1675 and SEQ ID NO: 1612, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1675 and SEQ ID NO: 1656, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1675 and SEQ ID NO: 1619, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1675 and SEQ ID NO: 1645, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1675 and SEQ ID NO: 1598, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1675 and SEQ ID NO: 1599, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1675 and SEQ ID NO: 1663, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1675 and SEQ ID NO: 1677, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1675 and SEQ ID NO: 1626, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1645 and SEQ ID NO: 1638, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1645 and SEQ ID NO: 1647, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1645 and SEQ ID NO: 1609, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1645 and SEQ ID NO: 1621, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1645 and SEQ ID NO: 1617, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1645 and SEQ ID NO: 1654, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1645 and SEQ ID NO: 1631, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1645 and SEQ ID NO: 1620, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1645 and SEQ ID NO: 1637, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1645 and SEQ ID NO: 1612, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1645 and SEQ ID NO: 1656, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1645 and SEQ ID NO: 1619, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1645 and SEQ ID NO: 1675, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1598 and SEQ ID NO: 1638, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1598 and SEQ ID NO: 1647, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1598 and SEQ ID NO: 1609, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1598 and SEQ ID NO: 1621, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1598 and SEQ ID NO: 1617, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1598 and SEQ ID NO: 1654, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1598 and SEQ ID NO: 1631, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1598 and SEQ ID NO: 1620, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1598 and SEQ ID NO: 1637, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1598 and SEQ ID NO: 1612, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1598 and SEQ ID NO: 1656, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1598 and SEQ ID NO: 1619, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1598 and SEQ ID NO: 1675, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1598 and SEQ ID NO: 1645, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1598 and SEQ ID NO: 1599, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1598 and SEQ ID NO: 1663, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1598 and SEQ ID NO: 1677, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1598 and SEQ ID NO: 1626, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1599 and SEQ ID NO: 1638, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1599 and SEQ ID NO: 1647, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1599 and SEQ ID NO: 1609, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1599 and SEQ ID NO: 1621, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1599 and SEQ ID NO: 1617, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1599 and SEQ ID NO: 1654, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1599 and SEQ ID NO: 1631, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1599 and SEQ ID NO: 1620, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1599 and SEQ ID NO: 1637, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1599 and SEQ ID NO: 1612, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1599 and SEQ ID NO: 1656, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1599 and SEQ ID NO: 1619, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1599 and SEQ ID NO: 1675, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1599 and SEQ ID NO: 1645, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1599 and SEQ ID NO: 1598, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1599 and SEQ ID NO: 1663, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1599 and SEQ ID NO: 1677, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1599 and SEQ ID NO: 1626, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1663 and SEQ ID NO: 1638, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1663 and SEQ ID NO: 1647, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1663 and SEQ ID NO: 1609, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1663 and SEQ ID NO: 1621, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1663 and SEQ ID NO: 1617, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1663 and SEQ ID NO: 1654, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1663 and SEQ ID NO: 1631, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1663 and SEQ ID NO: 1620, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1663 and SEQ ID NO: 1637, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1663 and SEQ ID NO: 1612, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1663 and SEQ ID NO: 1656, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1663 and SEQ ID NO: 1619, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1663 and SEQ ID NO: 1675, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1663 and SEQ ID NO: 1645, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1663 and SEQ ID NO: 1598, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1663 and SEQ ID NO: 1599, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1663 and SEQ ID NO: 1677, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1663 and SEQ ID NO: 1626, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1677 and SEQ ID NO: 1638, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1677 and SEQ ID NO: 1647, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1677 and SEQ ID NO: 1609, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1677 and SEQ ID NO: 1621, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1677 and SEQ ID NO: 1617, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1677 and SEQ ID NO: 1654, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1677 and SEQ ID NO: 1631, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1677 and SEQ ID NO: 1620, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1677 and SEQ ID NO: 1637, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1677 and SEQ ID NO: 1612, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1677 and SEQ ID NO: 1656, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1677 and SEQ ID NO: 1619, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1677 and SEQ ID NO: 1675, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1677 and SEQ ID NO: 1645, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1677 and SEQ ID NO: 1598, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1677 and SEQ ID NO: 1599, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1677 and SEQ ID NO: 1663, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1677 and SEQ ID NO: 1626, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1626 and SEQ ID NO: 1638, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1626 and SEQ ID NO: 1647, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1626 and SEQ ID NO: 1609, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1626 and SEQ ID NO: 1621, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1626 and SEQ ID NO: 1617, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1626 and SEQ ID NO: 1654, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1626 and SEQ ID NO: 1631, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1626 and SEQ ID NO: 1620, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1626 and SEQ ID NO: 1637, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1626 and SEQ ID NO: 1612, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1626 and SEQ ID NO: 1656, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1626 and SEQ ID NO: 1619, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1626 and SEQ ID NO: 1675, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1626 and SEQ ID NO: 1645, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1626 and SEQ ID NO: 1598, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1626 and SEQ ID NO: 1599, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1626 and SEQ ID NO: 1663, respectively. In an aspect, the first gRNA molecule and the second gRNA molecule include targeting domains comprising, e.g., consisting of, SEQ ID NO: 1626 and SEQ ID NO: 1677, respectively.

III. Methods for Designing gRNAs

Methods for designing gRNAs are described herein, including methods for selecting, designing and validating target sequences. Exemplary targeting domains are also provided herein. Targeting Domains discussed herein can be incorporated into the gRNAs described herein.

Methods for selection and validation of target sequences as well as off-target analyses are described, e.g., in. Mali el al., 2013 SCIENCE 339(6121): 823-826; Hsu et al, 2013 NAT BIOTECHNOL, 31 (9): 827-32; Fu et al, 2014 NAT BIOTECHNOL, doi: 10.1038/nbt.2808. PubMed PM ID: 24463574; Heigwer et al, 2014 NAT METHODS 11(2): 122-3. doi: 10.1038/nmeth.2812. PubMed PMID: 24481216; Bae el al, 2014 BIOINFORMATICS PubMed PMID: 24463181; Xiao A el al, 2014 BIOINFORMATICS PubMed PMID: 24389662.

For example, a software tool can be used to optimize the choice of gRNA within a user's target sequence, e.g., to minimize total off-target activity across the genome. Off target activity may be other than cleavage. For each possible gRNA choice e.g., using S. pyogenes Cas9, the tool can identify all off-target sequences (e.g., preceding either NAG or NGG PAMs) across the genome that contain up to certain number (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10) of mismatched base-pairs. The cleavage efficiency at each off-target sequence can be predicted, e.g., using an experimentally-derived weighting scheme. Each possible gRNA is then ranked according to its total predicted off-target cleavage; the top-ranked gRNAs represent those that are likely to have the greatest on-target and the least off-target cleavage. Other functions, e.g., automated reagent design for CRISPR construction, primer design for the on-target Surveyor assay, and primer design for high-throughput detection and quantification of off-target cleavage via next-gen sequencing, can also be included in the tool. Candidate gRNA molecules can be evaluated by art-known methods or as described herein.

Although software algorithms may be used to generate an initial list of potential gRNA molecules, cutting efficiency and specificity will not necessarily reflect the predicted values, and gRNA molecules typically require screening in specific cell lines, e.g., primary human cell lines, e.g., human HSPCs, e.g., human CD34+ cells, to determine, for example, cutting efficiency, indel formation, cutting specificity and change in desired phenotype. These properties may be assayed by the methods described herein.

In aspects of the invention, a gRNA comprising the targeting domain of CR00312 (SEQ ID NO: 248, underlined below), e.g., one of the gRNA molecules described below, is useful in the CRISPR systems, methods, cells and other aspects and embodiments of the invention, including in aspects involving more than one gRNA molecule, e.g., described herein:

sgRNA CR00312 #1: (SEQ ID NO: 342) GUUUGGCCUCUGAUUAGGGUGUUUUAGAGCUAGAAAUAGCAAGUUAAAAU AAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU sgRNA CR00312 #2: (SEQ ID NO: 343) mG*mU*mU*UGGCCUCUGAUUAGGGUGUUUUAGAGCUAGAAAUAGCAAGU UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU GCU*mU*mU*mU sgRNA CR00312 #3: (SEQ ID NO: 1762)) mG*mU*mU*UGGCCUCUGAUUAGGGUGUUUUAGAGCUAGAAAUAGCAAGU UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU GCmU*mU*mU*U dgRNA CR00312 #1: crRNA: (SEQ ID NO: 344) GUUUGGCCUCUGAUUAGGGUGUUUUAGAGCUAUGCUGUUUUG tracr: (SEQ ID NO: 6660) AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG UGGCACCGAGUCGGUGCUUUUUUU dgRNA CR00312 #2: crRNA: (SEQ ID NO: 345) mG*mU*mU*UGGCCUCUGAUUAGGGUGUUUUAGAGCUAUGCUGUU*mU*m U*mG tracr: (SEQ ID NO: 346) mA*mA*mC*AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUG AAAAAGUGGCACCGAGUCGGUGCUUUU*mU*mU*mU dgRNA CR00312 #3: crRNA: (SEQ ID NO: 345) mG*mU*mU*UGGCCUCUGAUUAGGGUGUUUUAGAGCUAUGCUGUU*mU*m U*mG tracr: (SEQ ID NO: 6660) AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG UGGCACCGAGUCGGUGCUUUUUUU.

In aspects of the invention, a gRNA comprising the targeting domain of CR001128 (SEQ ID NO: 338, underlined below), e.g., one of the gRNA molecules described below, is useful in the CRISPR systems, methods, cells and other aspects and embodiments of the invention, including in aspects involving more than one gRNA molecule, e.g., described herein:

sgRNA CR001128 #1: (SEQ ID NO: 347) AUCAGAGGCCAAACCCUUCCGUUUUAGAGCUAGAAAUAGCAAGUUAAAAU AAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU sgRNA CR001128 #2: (SEQ ID NO: 348) mA*mU*mC*AGAGGCCAAACCCUUCCGUUUUAGAGCUAGAAAUAGCAAGU UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU GCU*mU*mU*mU sgRNA CR001128 #3: (SEQ ID NO: 1763) mA*mU*mC*AGAGGCCAAACCCUUCCGUUUUAGAGCUAGAAAUAGCAAGU UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU GCmU*mU*mU*U dgRNA CR001128 #1: crRNA: (SEQ ID NO: 349) AUCAGAGGCCAAACCCUUCCGUUUUAGAGCUAUGCUGUUUUG tracr: (SEQ ID NO: 6660) AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG UGGCACCGAGUCGGUGCUUUUUUU dgRNA CR001128 #2: crRNA: (SEQ ID NO: 350) mA*mU*mC*AGAGGCCAAACCCUUCCGUUUUAGAGCUAUGCUGUU*mU*m U*mG tracr: (SEQ ID NO: 346) mA*mA*mC*AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUG AAAAAGUGGCACCGAGUCGGUGCUUUU*mU*mU*mU dgRNA CR001128 #3: crRNA: (SEQ ID NO: 350) mA*mU*mC*AGAGGCCAAACCCUUCCGUUUUAGAGCUAUGCUGUU*mU*m U*mG tracr: (SEQ ID NO: 6660) AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG UGGCACCGAGUCGGUGCUUUUUUU.

In aspects of the invention, a gRNA comprising the targeting domain of CR001126 (SEQ ID NO: 336, underlined below), e.g., one of the gRNA molecules described below, is useful in the CRISPR systems, methods, cells and other aspects and embodiments of the invention, including in aspects involving more than one gRNA molecule, e.g., described herein:

sgRNA CR001126 #1: (SEQ ID NO: 351) UUUAUCACAGGCUCCAGGAAGUUUUAGAGCUAGAAAUAGCAAGUUAAAAU AAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU sgRNA CR001126 #2: (SEQ ID NO: 352) mU*mU*mU*AUCACAGGCUCCAGGAAGUUUUAGAGCUAGAAAUAGCAAGU UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU GCU*mU*mU*mU sgRNA CR001126 #3: (SEQ ID NO: 1764) mU*mU*mU*AUCACAGGCUCCAGGAAGUUUUAGAGCUAGAAAUAGCAAGU UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU GCmU*mU*mU*U dgRNA CR001126 #1: crRNA: (SEQ ID NO: 353) UUUAUCACAGGCUCCAGGAAGUUUUAGAGCUAUGCUGUUUUG tracr: (SEQ ID NO: 6660) AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG UGGCACCGAGUCGGUGCUUUUUUU dgRNA CR001126 #2: crRNA: (SEQ ID NO: 354) mU*mU*mU*AUCACAGGCUCCAGGAAGUUUUAGAGCUAUGCUGUU*mU*m U*mG tracr: (SEQ ID NO: 346) mA*mA*mC*AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUG AAAAAGUGGCACCGAGUCGGUGCUUUU*mU*mU*mU dgRNA CR001126 #3: crRNA: (SEQ ID NO: 354) mU*mU*mU*AUCACAGGCUCCAGGAAGUUUUAGAGCUAUGCUGUU*mU*m U*mG tracr: (SEQ ID NO: 6660) AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG UGGCACCGAGUCGGUGCUUUUUUU.

In aspects of the invention, a gRNA comprising the targeting domain of CR00311 (SEQ ID NO: 247, underlined below), e.g., one of the gRNA molecules described below, is useful in the CRISPR systems, methods, cells and other aspects and embodiments of the invention, including in aspects involving more than one gRNA molecule, e.g., described herein:

sgRNA CR00311 #1: (SEQ ID NO: 355) UUUGGCCUCUGAUUAGGGUGGUUUUAGAGCUAGAAAUAGCAAGUUAAAAU AAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU sgRNA CR00311 #2: (SEQ ID NO: 356) mU*mU*mU*GGCCUCUGAUUAGGGUGGUUUUAGAGCUAGAAAUAGCAAGU UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU GCU*mU*mU*mU sgRNA CR00311 #3: (SEQ ID NO: 1765) mU*mU*mU*GGCCUCUGAUUAGGGUGGUUUUAGAGCUAGAAAUAGCAAGU UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU GCmU*mU*mU*U dgRNA CR00311 #1: crRNA: (SEQ ID NO: 357) UUUGGCCUCUGAUUAGGGUGGUUUUAGAGCUAUGCUGUUUUG tracr: (SEQ ID NO: 6660) AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG UGGCACCGAGUCGGUGCUUUUUUU dgRNA CR00311 #2: crRNA: (SEQ ID NO: 358) mU*mU*mU*GGCCUCUGAUUAGGGUGGUUUUAGAGCUAUGCUGUU*mU*m U*mG tracr: (SEQ ID NO: 346) mA*mA*mC*AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUG AAAAAGUGGCACCGAGUCGGUGCUUUU*mU*mU*mU dgRNA CR00311 #3: crRNA: (SEQ ID NO: 358) mU*mU*mU*GGCCUCUGAUUAGGGUGGUUUUAGAGCUAUGCUGUU*mU*m U*mG tracr: (SEQ ID NO: 6660) AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG UGGCACCGAGUCGGUGCUUUUUUU.

In aspects of the invention, a gRNA comprising the targeting domain of CR00309 (SEQ ID NO: 245, underlined below), e.g., one of the gRNA molecules described below, is useful in the CRISPR systems, methods, cells and other aspects and embodiments of the invention, including in aspects involving more than one gRNA molecule, e.g., described herein:

sgRNA CR00309 #1: (SEQ ID NO: 359) CACGCCCCCACCCUAAUCAGGUUUUAGAGCUAGAAAUAGCAAGUUAAAAU AAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU sgRNA CR00309 #2: (SEQ ID NO: 360) mC*mA*mC*GCCCCCACCCUAAUCAGGUUUUAGAGCUAGAAAUAGCAAGU UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU GCU*mU*mU*mU sgRNA CR00309 #3: (SEQ ID NO: 1766) mC*mA*mC*GCCCCCACCCUAAUCAGGUUUUAGAGCUAGAAAUAGCAAGU UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU GCmU*mU*mU*U dgRNA CR00309 #1: crRNA: (SEQ ID NO: 361) CACGCCCCCACCCUAAUCAGGUUUUAGAGCUAUGCUGUUUUG tracr: (SEQ ID NO: 6660) AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG UGGCACCGAGUCGGUGCUUUUUUU dgRNA CR00309 #2: crRNA: (SEQ ID NO: 362) mC*mA*mC*GCCCCCACCCUAAUCAGGUUUUAGAGCUAUGCUGUU*mU*m U*mG tracr: (SEQ ID NO: 346) mA*mA*mC*AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUG AAAAAGUGGCACCGAGUCGGUGCUUUU*mU*mU*mU dgRNA CR00309 #3: crRNA: (SEQ ID NO: 362) mC*mA*mC*GCCCCCACCCUAAUCAGGUUUUAGAGCUAUGCUGUU*mU*m U*mG tracr: (SEQ ID NO: 6660) AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG UGGCACCGAGUCGGUGCUUUUUUU.

In aspects of the invention, a gRNA comprising the targeting domain of CR001127 (SEQ ID NO: 337, underlined below), e.g., one of the gRNA molecules described below, is useful in the CRISPR systems, methods, cells and other aspects and embodiments of the invention, including in aspects involving more than one gRNA molecule, e.g., described herein:

sgRNA CR001127 #1: (SEQ ID NO: 363) CACAGGCUCCAGGAAGGGUUGUUUUAGAGCUAGAAAUAGCAAGUUAAAAU AAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU sgRNA CR001127 #2: (SEQ ID NO: 364) mC*mA*mC*AGGCUCCAGGAAGGGUUGUUUUAGAGCUAGAAAUAGCAAGU UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU GCU*mU*mU*mU sgRNA CR001127 #3: (SEQ ID NO: 1767) mC*mA*mC*AGGCUCCAGGAAGGGUUGUUUUAGAGCUAGAAAUAGCAAGU UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU GCmU*mU*mU*U dgRNA CR001127 #1: crRNA: (SEQ ID NO: 365) CACAGGCUCCAGGAAGGGUUGUUUUAGAGCUAUGCUGUUUUG tracr: (SEQ ID NO: 6660) AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG UGGCACCGAGUCGGUGCUUUUUUU dgRNA CR001127 #2: crRNA: (SEQ ID NO: 366) mC*mA*mC*AGGCUCCAGGAAGGGUUGUUUUAGAGCUAUGCUGUU*mU*m U*mG tracr: (SEQ ID NO: 346) mA*mA*mC*AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUG AAAAAGUGGCACCGAGUCGGUGCUUUU*mU*mU*mU dgRNA CR001127 #3: crRNA: (SEQ ID NO: 366) mC*mA*mC*AGGCUCCAGGAAGGGUUGUUUUAGAGCUAUGCUGUU*mU*m U*mG tracr: (SEQ ID NO: 6660) AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG UGGCACCGAGUCGGUGCUUUUUUU.

In aspects of the invention, a gRNA comprising the targeting domain of CR00316 (SEQ ID NO: 252, underlined below), e.g., one of the gRNA molecules described below, is useful in the CRISPR systems, methods, cells and other aspects and embodiments of the invention, including in aspects involving more than one gRNA molecule, e.g., described herein:

sgRNA CR00316 #1: (SEQ ID NO: 367) UUGCUUUUAUCACAGGCUCCGUUUUAGAGCUAGAAAUAGCAAGUUAAAAU AAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU sgRNA CR00316 #2: (SEQ ID NO: 368) mU*mU*mG*CUUUUAUCACAGGCUCCGUUUUAGAGCUAGAAAUAGCAAGU UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU GCU*mU*mU*mU sgRNA CR00316 #3: (SEQ ID NO: 1768) mU*mU*mG*CUUUUAUCACAGGCUCCGUUUUAGAGCUAGAAAUAGCAAGU UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU GCmU*mU*mU*U dgRNA CR00316 #1: crRNA: (SEQ ID NO: 369) UUGCUUUUAUCACAGGCUCCGUUUUAGAGCUAUGCUGUUUUG tracr: (SEQ ID NO: 6660) AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG UGGCACCGAGUCGGUGCUUUUUUU dgRNA CR00316 #2: crRNA: (SEQ ID NO: 370) mU*mU*mG*CUUUUAUCACAGGCUCCGUUUUAGAGCUAUGCUGUU*mU*m U*mG tracr: (SEQ ID NO: 346) mA*mA*mC*AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUG AAAAAGUGGCACCGAGUCGGUGCUUUU*mU*mU*mU dgRNA CR00316 #3: crRNA: (SEQ ID NO: 370) mU*mU*mG*CUUUUAUCACAGGCUCCGUUUUAGAGCUAUGCUGUU*mU*m U*mG tracr: (SEQ ID NO: 6660) AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG UGGCACCGAGUCGGUGCUUUUUUU.

In aspects of the invention, a gRNA comprising the targeting domain of CR001125 (SEQ ID NO: 335, underlined below), e.g., one of the gRNA molecules described below, is useful in the CRISPR systems, methods, cells and other aspects and embodiments of the invention, including in aspects involving more than one gRNA molecule, e.g., described herein:

sgRNA CR001125 #1: (SEQ ID NO: 371) UUUUAUCACAGGCUCCAGGAGUUUUAGAGCUAGAAAUAGCAAGUUAAAAU AAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU sgRNA CR001125 #2: (SEQ ID NO: 372) mU*mU*mU*UAUCACAGGCUCCAGGAGUUUUAGAGCUAGAAAUAGCAAGU UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU GCU*mU*mU*mU sgRNA CR001125 #3: (SEQ ID NO: 1769) mU*mU*mU*UAUCACAGGCUCCAGGAGUUUUAGAGCUAGAAAUAGCAAGU UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU GCmU*mU*mU*U dgRNA CR001125 #1: crRNA: (SEQ ID NO: 373) UUUUAUCACAGGCUCCAGGAGUUUUAGAGCUAUGCUGUUUUG tracr: (SEQ ID NO: 6660) AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG UGGCACCGAGUCGGUGCUUUUUUU dgRNA CR001125 #2: crRNA: (SEQ ID NO: 374) mU*mU*mU*UAUCACAGGCUCCAGGAGUUUUAGAGCUAUGCUGUU*mU*m U*mG tracr: (SEQ ID NO: 346) mA*mA*mC*AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUG AAAAAGUGGCACCGAGUCGGUGCUUUU*mU*mU*mU dgRNA CR001125 #3: crRNA: (SEQ ID NO: 374) mU*mU*mU*UAUCACAGGCUCCAGGAGUUUUAGAGCUAUGCUGUU*mU*m U*mG tracr: (SEQ ID NO: 6660) AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG UGGCACCGAGUCGGUGCUUUUUUU.

In aspects of the invention, a gRNA comprising the targeting domain of CR001030 (SEQ ID NO: 100, underlined below), e.g., one of the gRNA molecules described below, is useful in the CRISPR systems, methods, cells and other aspects and embodiments of the invention, including in aspects involving more than one gRNA molecule, e.g., described herein:

sgRNA CR001030 #1: (SEQ ID NO: 375) ACUGCUGAAAGAGAUGCGGUGUUUUAGAGCUAGAAAUAGCAAGUUAAAAU AAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU sgRNA CR001030 #2: (SEQ ID NO: 376) mA*mC*mU*GCUGAAAGAGAUGCGGUGUUUUAGAGCUAGAAAUAGCAAGU UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU GCU*mU*mU*mU sgRNA CR001030 #3: (SEQ ID NO: 1770) mA*mC*mU*GCUGAAAGAGAUGCGGUGUUUUAGAGCUAGAAAUAGCAAGU UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU GCmU*mU*mU*U dgRNA CR001030 #1: (SEQ ID NO: 377) crRNA: ACUGCUGAAAGAGAUGCGGUGUUUUAGAGCUAUGCUGUUUUG tracr: (SEQ ID NO: 6660) AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG UGGCACCGAGUCGGUGCUUUUUUU dgRNA CR001030 #2: crRNA: (SEQ ID NO: 378) mA*mC*mU*GCUGAAAGAGAUGCGGUGUUUUAGAGCUAUGCUGUU*mU*m U*mG tracr: (SEQ ID NO: 346) mA*mA*mC*AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUG AAAAAGUGGCACCGAGUCGGUGCUUUU*mU*mU*mU dgRNA CR001030 #3: crRNA: (SEQ ID NO: 378) mA*mC*mU*GCUGAAAGAGAUGCGGUGUUUUAGAGCUAUGCUGUU*mU*m U*mG tracr: (SEQ ID NO: 6660) AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG UGGCACCGAGUCGGUGCUUUUUUU.

In aspects of the invention, a gRNA comprising the targeting domain of CR001028 (SEQ ID NO: 98, underlined below), e.g., one of the gRNA molecules described below, is useful in the CRISPR systems, methods, cells and other aspects and embodiments of the invention, including in aspects involving more than one gRNA molecule, e.g., described herein:

sgRNA CR001028 #1: (SEQ ID NO: 379) UGCGGUGGGGAGAUAUGUAGGUUUUAGAGCUAGAAAUAGCAAGUUAAAAU AAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU sgRNA CR001028 #2: (SEQ ID NO: 380) mU*mG*mC*GGUGGGGAGAUAUGUAGGUUUUAGAGCUAGAAAUAGCAAGU UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU GCU*mU*mU*mU sgRNA CR001028 #3: (SEQ ID NO: 1771) mU*mG*mC*GGUGGGGAGAUAUGUAGGUUUUAGAGCUAGAAAUAGCAAGU UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU GCmU*mU*mU*U dgRNA CR001028 #1: (SEQ ID NO: 381) crRNA: UGCGGUGGGGAGAUAUGUAGGUUUUAGAGCUAUGCUGUUUUG tracr: (SEQ ID NO: 6660) AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG UGGCACCGAGUCGGUGCUUUUUUU dgRNA CR001028 #2: crRNA: (SEQ ID NO: 382) mU*mG*mC*GGUGGGGAGAUAUGUAGGUUUUAGAGCUAUGCUGUU*mU*m U*mG tracr: (SEQ ID NO: 346) mA*mA*mC*AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUG AAAAAGUGGCACCGAGUCGGUGCUUUU*mU*mU*mU dgRNA CR001028 #3: crRNA: (SEQ ID NO: 382) mU*mG*mC*GGUGGGGAGAUAUGUAGGUUUUAGAGCUAUGCUGUU*mU*m U*mG tracr: (SEQ ID NO: 6660) AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG UGGCACCGAGUCGGUGCUUUUUUU.

In aspects of the invention, a gRNA comprising the targeting domain of CR001221 (SEQ ID NO: 1589, underlined below), e.g., one of the gRNA molecules described below, is useful in the CRISPR systems, methods, cells and other aspects and embodiments of the invention, including in aspects involving more than one gRNA molecule, e.g., described herein:

sgRNA CR001221 #1: (SEQ ID NO: 383) GAAACAAUGAGGACCUGACUGUUUUAGAGCUAGAAAUAGCAAGUUAAAAU AAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU sgRNA CR001221 #2: (SEQ ID NO: 384) mG*mA*mA*ACAAUGAGGACCUGACUGUUUUAGAGCUAGAAAUAGCAAGU UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU GCU*mU*mU*mU sgRNA CR001221 #3: (SEQ ID NO: 1772) mG*mA*mA*ACAAUGAGGACCUGACUGUUUUAGAGCUAGAAAUAGCAAGU UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU GCmU*mU*mU*U dgRNA CR001221 #1: (SEQ ID NO: 385) crRNA: GAAACAAUGAGGACCUGACUGUUUUAGAGCUAUGCUGUUUUG tracr: (SEQ ID NO: 6660) AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG UGGCACCGAGUCGGUGCUUUUUUU dgRNA CR001221 #2: crRNA: (SEQ ID NO: 386) mG*mA*mA*ACAAUGAGGACCUGACUGUUUUAGAGCUAUGCUGUU*mU*m U*mG tracr: (SEQ ID NO: 346) mA*mA*mC*AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUG AAAAAGUGGCACCGAGUCGGUGCUUUU*mU*mU*mU dgRNA CR001221 #3: crRNA: (SEQ ID NO: 386) mG*mA*mA*ACAAUGAGGACCUGACUGUUUUAGAGCUAUGCUGUU*mU*m U*mG tracr: (SEQ ID NO: 6660) AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG UGGCACCGAGUCGGUGCUUUUUUU.

In aspects of the invention, a gRNA comprising the targeting domain of CR001137 (SEQ ID NO: 1505, underlined below), e.g., one of the gRNA molecules described below, is useful in the CRISPR systems, methods, cells and other aspects and embodiments of the invention, including in aspects involving more than one gRNA molecule, e.g., described herein:

sgRNA CR001137 #1: (SEQ ID NO: 387) GUAAGCAUUUAAGUGGCUACGUUUUAGAGCUAGAAAUAGCAAGUUAAAAU AAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU sgRNA CR001137 #2: (SEQ ID NO: 388) mG*mU*mA*AGCAUUUAAGUGGCUACGUUUUAGAGCUAGAAAUAGCAAGU UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU GCU*mU*mU*mU sgRNA CR001137 #3: (SEQ ID NO: 1773) mG*mU*mA*AGCAUUUAAGUGGCUACGUUUUAGAGCUAGAAAUAGCAAGU UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU GCmU*mU*mU*U dgRNA CR001137 #1: (SEQ ID NO: 389) crRNA: GUAAGCAUUUAAGUGGCUACGUUUUAGAGCUAUGCUGUUUUG tracr: (SEQ ID NO: 6660) AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG UGGCACCGAGUCGGUGCUUUUUUU dgRNA CR001137 #2: crRNA: (SEQ ID NO: 390) mG*mU*mA*AGCAUUUAAGUGGCUACGUUUUAGAGCUAUGCUGUU*mU*m U*mG tracr: (SEQ ID NO: 346) mA*mA*mC*AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUG AAAAAGUG GCACCGAGUCGGUGCUUUU*mU*mU*mU dgRNA CR001137 #3: crRNA: (SEQ ID NO: 390) mG*mU*mA*AGCAUUUAAGUGGCUACGUUUUAGAGCUAUGCUGUU*mU*m U*mG tracr: (SEQ ID NO: 6660) AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG UGGCACCGAGUCGGUGCUUUUUUU.

In aspects of the invention, a gRNA comprising the targeting domain of CR003035 (SEQ ID NO: 1505, underlined below), e.g., one of the gRNA molecules described below, is useful in the CRISPR systems, methods, cells and other aspects and embodiments of the invention, including in aspects involving more than one gRNA molecule, e.g., described herein:

sgRNA CR003035 #1: (SEQ ID NO: 391) AGGCACCUCAGACUCAGCAUGUUUUAGAGCUAGAAAUAGCAAGUUAAAAU AAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU sgRNA CR003035 #2: (SEQ ID NO: 392) mA*mG*mG*CACCUCAGACUCAGCAGUUUUAGAGCUAGAAAUAGCAAGU UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU GCU*mU*mU*mU sgRNA CR003035 #3: (SEQ ID NO: 1774) mA*mG*mG*CACCUCAGACUCAGCAUGUUUUAGAGCUAGAAAUAGCAAGU UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU GCmU*mU*mU*U dgRNA CR003035 #1: (SEQ ID NO: 393) crRNA: AGGCACCUCAGACUCAGCAUGUUUUAGAGCUAUGCUGUUUUG tracr: (SEQ ID NO: 6660) AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG UGGCACCGAGUCGGUGCUUUUUUU dgRNA CR003035 #2: (SEQ ID NO: 394) crRNA: mA*mG*mG*CACCUCAGACUCAGCAUGUUUUAGAGCUAUGCUG UU*mU*mU*mG tracr: (SEQ ID NO: 346) mA*mA*mC*AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUG AAAAAGUGGCACCGAGUCGGUGCUUUU*mU*mU*mU dgRNA CR003035 #3: (SEQ ID NO: 394) crRNA: mA*mG*mG*CACCUCAGACUCAGCAUGUUUUAGAGCUAUGCUG UU*mU*mU*mG tracr: (SEQ ID NO: 6660) AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG UGGCACCGAGUCGGUGCUUUUUUU.

In aspects of the invention, a gRNA comprising the targeting domain of CR003085 (SEQ ID NO: 1750, underlined below), e.g., one of the gRNA molecules described below, is useful in the CRISPR systems, methods, cells and other aspects and embodiments of the invention, including in aspects involving more than one gRNA molecule, e.g., described herein:

sgRNA CR003085 #1: (SEQ ID NO: 395) AUGGUAUGGGAGGUAUACUAGUUUUAGAGCUAGAAAUAGCAAGUUAAAAU AAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU sgRNA CR003085 #2: (SEQ ID NO: 396) mA*mU*mG*GUAUGGGAGGUAUACUAGUUUUAGAGCUAGAAAUAGCAAGU UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU GCU*mU*mU*mU sgRNA CR003085 #3: (SEQ ID NO: 1775) mA*mU*mG*GUAUGGGAGGUAUACUAGUUUUAGAGCUAGAAAUAGCAAGU UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU GCmU*mU*mU*U dgRNA CR003085 #1: (SEQ ID NO: 397) crRNA: AUGGUAUGGGAGGUAUACUAGUUUUAGAGCUAUGCUGUUUUG tracr: (SEQ ID NO: 6660) AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG UGGCACCGAGUCGGUGCUUUUUUU dgRNA CR003085 #2: crRNA: (SEQ ID NO: 398) mA*mU*mG*GUAUGGGAGGUAUACUAGUUUUAGAGCUAUGCUGUU*mU*m U*mG tracr: (SEQ ID NO: 346) mA*mA*mC*AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUG AAAAAGUGGCACCGAGUCGGUGCUUUU*mU*mU*mU dgRNA CR003085 #3: crRNA: (SEQ ID NO: 398) mA*mU*mG*GUAUGGGAGGUAUACUAGUUUUAGAGCUAUGCUGUU*mU*m U*mG tracr: (SEQ ID NO: 6660) AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAG UGGCACCGAGUCGGUGCUUUUUUU.

In each of the gRNA molecules described above, a “*” denotes a phosphorothioate bond between the adjacent nucleotides, and “mN” (where N=A, G, C or U) denotes a 2′-OMe modified nucleotide. In embodiments, any of the gRNA molecules described herein, e.g., described above, is complexed with a Cas9 molecule, e.g., as described herein, to form a ribonuclear protein complex (RNP). Such RNPs are particularly useful in the methods, cells, and other aspects and embodiments of the invention, e.g., described herein.

IV. Cas Molecules Cas9 Molecules

In preferred embodiments, the Cas molecule is a Cas9 molecule. Cas9 molecules of a variety of species can be used in the methods and compositions described herein. While the S. pyogenes Cas9 molecule are the subject of much of the disclosure herein, Cas9 molecules of, derived from, or based on the Cas9 proteins of other species listed herein can be used as well. In other words, other Cas9 molecules, e.g., S. thermophilus, Staphylococcus aureus and/or Neisseria meningitidis Cas9 molecules, may be used in the systems, methods and compositions described herein. Additional Cas9 species include: Acidovorax avenae, Actinobacillus pleuropneumoniae, Actinobacillus succinogenes, Actinobacillus suis, Actinomyces sp., cycliphilus denitrificans, Aminomonas paucivorans, Bacillus cereus, Bacillus smithii, Bacillus thuringiensis, Bacteroides sp., Blastopirellula marina, Bradyrhiz obium sp., Brevibacillus latemsporus, Campylobacter coli, Campylobacter jejuni, Campylobacter lad, Candidatus Puniceispirillum, Clostridiu cellulolyticum, Clostridium perfringens, Corynebacterium accolens, Corynebacterium diphtheria, Corynebacterium matruchotii, Dinoroseobacter sliibae, Eubacterium dolichum, gamma proteobacterium, Gluconacetobacler diazotrophicus, Haemophilus parainfluenzae, Haemophilus sputorum, Helicobacter canadensis, Helicobacter cinaedi, Helicobacter mustelae, Ilyobacler polytropus, Kingella kingae, Lactobacillus crispatus, Listeria ivanovii, Listeria monocytogenes, Listeriaceae bacterium, Methylocystis sp., Methylosinus trichosporium, Mobiluncus mulieris, Neisseria bacilliformis, Neisseria cinerea, Neisseria flavescens, Neisseria lactamica. Neisseria sp., Neisseria wadsworthii, Nitrosomonas sp., Parvibaculum lavamentivorans, Pasteurella multocida, Phascolarctobacterium succinatutens, Ralstonia syzygii, Rhodopseudomonas palustris, Rhodovulum sp., Simonsiella muelleri, Sphingomonas sp., Sporolactobacillus vineae, Staphylococcus lugdunensis, Streptococcus sp., Subdoligranulum sp., Tislrella mobilis, Treponema sp., or Verminephrobacter eiseniae.

A Cas9 molecule, as that term is used herein, refers to a molecule that can interact with a gRNA molecule (e.g., sequence of a domain of a tracr) and, in concert with the gRNA molecule, localize (e.g., target or home) to a site which comprises a target sequence and PAM sequence.

In an embodiment, the Cas9 molecule is capable of cleaving a target nucleic acid molecule, which may be referred to herein as an active Cas9 molecule. In an embodiment, an active Cas9 molecule, comprises one or more of the following activities: a nickase activity, i.e., the ability to cleave a single strand, e.g., the non-complementary strand or the complementary strand, of a nucleic acid molecule; a double stranded nuclease activity, i.e., the ability to cleave both strands of a double stranded nucleic acid and create a double stranded break, which in an embodiment is the presence of two nickase activities; an endonuclease activity; an exonuclease activity; and a helicase activity, i.e., the ability to unwind the helical structure of a double stranded nucleic acid.

In an embodiment, an enzymatically active Cas9 molecule cleaves both DNA strands and results in a double stranded break. In an embodiment, a Cas9 molecule cleaves only one strand, e.g., the strand to which the gRNA hybridizes to, or the strand complementary to the strand the gRNA hybridizes with. In an embodiment, an active Cas9 molecule comprises cleavage activity associated with an HNH-like domain. In an embodiment, an active Cas9 molecule comprises cleavage activity associated with an N-terminal RuvC-like domain. In an embodiment, an active Cas9 molecule comprises cleavage activity associated with an HNH-like domain and cleavage activity associated with an N-terminal RuvC-like domain. In an embodiment, an active Cas9 molecule comprises an active, or cleavage competent, HNH-like domain and an inactive, or cleavage incompetent, N-terminal RuvC-like domain. In an embodiment, an active Cas9 molecule comprises an inactive, or cleavage incompetent, HNH-like domain and an active, or cleavage competent, N-terminal RuvC-like domain.

In an embodiment, the ability of an active Cas9 molecule to interact with and cleave a target nucleic acid is PAM sequence dependent. A PAM sequence is a sequence in the target nucleic acid. In an embodiment, cleavage of the target nucleic acid occurs upstream from the PAM sequence. Active Cas9 molecules from different bacterial species can recognize different sequence motifs (e.g., PAM sequences). In an embodiment, an active Cas9 molecule of S. pyogenes recognizes the sequence motif NGG and directs cleavage of a target nucleic acid sequence 1 to 10, e.g., 3 to 5, base pairs upstream from that sequence. See, e.g., Mali el ai, SCIENCE 2013; 339(6121): 823-826. In an embodiment, an active Cas9 molecule of S. thermophilus recognizes the sequence motif NGGNG and NNAG AAW (W=A or T) and directs cleavage of a core target nucleic acid sequence 1 to 10, e.g., 3 to 5, base pairs upstream from these sequences. See, e.g., Horvath et al., SCIENCE 2010; 327(5962): 167-170, and Deveau et al, J BACTERIOL 2008; 190(4): 1390-1400. In an embodiment, an active Cas9 molecule of S mulans recognizes the sequence motif NGG or NAAR (R-A or G) and directs cleavage of a core target nucleic acid sequence 1 to 10, e.g., 3 to 5 base pairs, upstream from this sequence. See, e.g., Deveau et al., J BACTERIOL 2008; 190(4): 1390-1400.

In an embodiment, an active Cas9 molecule of S. aureus recognizes the sequence motif NNGRR (R=A or G) and directs cleavage of a target nucleic acid sequence 1 to 10, e.g., 3 to 5, base pairs upstream from that sequence. See, e.g., Ran F. et al., NATURE, vol. 520, 2015, pp. 186-191. In an embodiment, an active Cas9 molecule of N. meningitidis recognizes the sequence motif NNNNGATT and directs cleavage of a target nucleic acid sequence 1 to 10, e.g., 3 to 5, base pairs upstream from that sequence. See, e.g., Hou et al., PNAS EARLY EDITION 2013, 1-6. The ability of a Cas9 molecule to recognize a PAM sequence can be determined, e.g., using a transformation assay described in Jinek et al, SCIENCE 2012, 337:816.

Some Cas9 molecules have the ability to interact with a gRNA molecule, and in conjunction with the gRNA molecule home (e.g., targeted or localized) to a core target domain, but are incapable of cleaving the target nucleic acid, or incapable of cleaving at efficient rates. Cas9 molecules having no, or no substantial, cleavage activity may be referred to herein as an inactive Cas9 (an enzymatically inactive Cas9), a dead Cas9, or a dCas9 molecule. For example, an inactive Cas9 molecule can lack cleavage activity or have substantially less, e.g., less than 20, 10, 5, 1 or 0.1% of the cleavage activity of a reference Cas9 molecule, as measured by an assay described herein.

Exemplary naturally occurring Cas9 molecules are described in Chylinski et al, RNA Biology 2013; 10:5, 727-737. Such Cas9 molecules include Cas9 molecules of a cluster 1 bacterial family, cluster 2 bacterial family, cluster 3 bacterial family, cluster 4 bacterial family, cluster 5 bacterial family, cluster 6 bacterial family, a cluster 7 bacterial family, a cluster 8 bacterial family, a cluster 9 bacterial family, a cluster 10 bacterial family, a cluster 11 bacterial family, a cluster 12 bacterial family, a cluster 13 bacterial family, a cluster 14 bacterial family, a cluster 1 bacterial family, a cluster 16 bacterial family, a cluster 17 bacterial family, a cluster 18 bacterial family, a cluster 19 bacterial family, a cluster 20 bacterial family, a cluster 21 bacterial family, a cluster 22 bacterial family, a cluster 23 bacterial family, a cluster 24 bacterial family, a cluster 25 bacterial family, a cluster 26 bacterial family, a cluster 27 bacterial family, a cluster 28 bacterial family, a cluster 29 bacterial family, a cluster 30 bacterial family, a cluster 31 bacterial family, a cluster 32 bacterial family, a cluster 33 bacterial family, a cluster 34 bacterial family, a cluster 35 bacterial family, a cluster 36 bacterial family, a cluster 37 bacterial family, a cluster 38 bacterial family, a cluster 39 bacterial family, a cluster 40 bacterial family, a cluster 41 bacterial family, a cluster 42 bacterial family, a cluster 43 bacterial family, a cluster 44 bacterial family, a cluster 45 bacterial family, a cluster 46 bacterial family, a cluster 47 bacterial family, a cluster 48 bacterial family, a cluster 49 bacterial family, a cluster 50 bacterial family, a cluster 51 bacterial family, a cluster 52 bacterial family, a cluster 53 bacterial family, a cluster 54 bacterial family, a cluster 55 bacterial family, a cluster 56 bacterial family, a cluster 57 bacterial family, a cluster 58 bacterial family, a cluster 59 bacterial family, a cluster 60 bacterial family, a cluster 61 bacterial family, a cluster 62 bacterial family, a cluster 63 bacterial family, a cluster 64 bacterial family, a cluster 65 bacterial family, a cluster 66 bacterial family, a cluster 67 bacterial family, a cluster 68 bacterial family, a cluster 69 bacterial family, a cluster 70 bacterial family, a cluster 71 bacterial family, a cluster 72 bacterial family, a cluster 73 bacterial family, a cluster 74 bacterial family, a cluster 75 bacterial family, a cluster 76 bacterial family, a cluster 77 bacterial family, or a cluster 78 bacterial family.

Exemplary naturally occurring Cas9 molecules include a Cas9 molecule of a cluster 1 bacterial family. Examples include a Cas9 molecule of: S. pyogenes (e.g., strain SF370, MGAS 10270, MGAS 10750, MGAS2096, MGAS315, MGAS5005, MGAS6180, MGAS9429, NZ131 and SSI-1), S. thermophilus (e.g., strain LMD-9), S. pseudoporcinus (e.g., strain SPIN 20026), S. mutans (e.g., strain UA 159, NN2025), S. macacae (e.g., strain NCTC1 1558), S. gallolylicus (e.g., strain UCN34, ATCC BAA-2069), S. equines (e.g., strain ATCC 9812, MGCS 124), S. dysdalactiae (e.g., strain GGS 124), S. bovis (e.g., strain ATCC 700338), S. cmginosus (e.g.; strain F0211), S. agalactia* (e.g., strain NEM316, A909), Listeria monocytogenes (e.g., strain F6854), Listeria innocua (L. innocua, e.g., strain Clip 1 1262), EtUerococcus italicus (e.g., strain DSM 15952), or Enterococcus faecium (e.g., strain 1,231,408). Additional exemplary Cas9 molecules are a Cas9 molecule of Neisseria meningitidis (Hou et al. PNAS Early Edition 2013, 1-6) and a S. aureus Cas9 molecule.

In an embodiment, a Cas9 molecule, e.g., an active Cas9 molecule or inactive Cas9 molecule, comprises an amino acid sequence: having 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% homology with; differs at no more than 1%, 2%, 5%, 10%, 15%, 20%, 30%, or 40% of the amino acid residues when compared with; differs by at least 1, 2, 5, 10 or 20 amino acids but by no more than 100, 80, 70, 60, 50, 40 or 30 amino acids from; or is identical to; any Cas9 molecule sequence described herein or a naturally occurring Cas9 molecule sequence, e.g., a Cas9 molecule from a species listed herein or described in Chylinski et al., RNA Biology 2013, 10:5, ′I2′I-T,1 Hou et al. PNAS Early Edition 2013, 1-6.

In an embodiment, a Cas9 molecule comprises an amino acid sequence having 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% homology with; differs at no more than 1%, 2%, 5%, 10%, 15%, 20%, 30%, or 40% of the amino acid residues when compared with; differs by at least 1, 2, 5, 10 or 20 amino acids but by no more than 100, 80, 70, 60, 50, 40 or 30 amino acids from; or is identical to; S. pyogenes Cas9:

(SEQ ID NO: 6611) Met Asp Lys Lys Tyr Ser Ile Gly Leu Asp Ile Gly Thr Asn Ser Val 1               5                   10                  15 Gly Trp Ala Val Ile Thr Asp Glu Tyr Lys Val Pro Ser Lys Lys Phe             20                  25                  30 Lys Val Leu Gly Asn Thr Asp Arg His Ser Ile Lys Lys Asn Leu Ile         35                  40                  45 Gly Ala Leu Leu Phe Asp Ser Gly Glu Thr Ala Glu Ala Thr Arg Leu     50                  55                  60 Lys Arg Thr Ala Arg Arg Arg Tyr Thr Arg Arg Lys Asn Arg Ile Cys 65                  70                  75                  80 Tyr Leu Gln Glu Ile Phe Ser Asn Glu Met Ala Lys Val Asp Asp Ser                 85                  90                  95 Phe Phe His Arg Leu Glu Glu Ser Phe Leu Val Glu Glu Asp Lys Lys             100                 105                 110 His Glu Arg His Pro Ile Phe Gly Asn Ile Val Asp Glu Val Ala Tyr         115                 120                 125 His Glu Lys Tyr Pro Thr Ile Tyr His Leu Arg Lys Lys Leu Val Asp     130                 135                 140 Ser Thr Asp Lys Ala Asp Leu Arg Leu Ile Tyr Leu Ala Leu Ala His 145                 150                 155                 160 Met Ile Lys Phe Arg Gly His Phe Leu Ile Glu Gly Asp Leu Asn Pro                 165                 170                 175 Asp Asn Ser Asp Val Asp Lys Leu Phe Ile Gln Leu Val Gln Thr Tyr             180                 185                 190 Asn Gln Leu Phe Glu Glu Asn Pro Ile Asn Ala Ser Gly Val Asp Ala         195                 200                 205 Lys Ala Ile Leu Ser Ala Arg Leu Ser Lys Ser Arg Arg Leu Glu Asn     210                 215                 220 Leu Ile Ala Gln Leu Pro Gly Glu Lys Lys Asn Gly Leu Phe Gly Asn 225                 230                 235                 240 Leu Ile Ala Leu Ser Leu Gly Leu Thr Pro Asn Phe Lys Ser Asn Phe                 245                 250                 255 Asp Leu Ala Glu Asp Ala Lys Leu Gln Leu Ser Lys Asp Thr Tyr Asp             260                 265                 270 Asp Asp Leu Asp Asn Leu Leu Ala Gln Ile Gly Asp Gln Tyr Ala Asp         275                 280                 285 Leu Phe Leu Ala Ala Lys Asn Leu Ser Asp Ala Ile Leu Leu Ser Asp     290                 295                 300 Ile Leu Arg Val Asn Thr Glu Ile Thr Lys Ala Pro Leu Ser Ala Ser 305                 310                 315                 320 Met Ile Lys Arg Tyr Asp Glu His His Gln Asp Leu Thr Leu Leu Lys                 325                 330                 335 Ala Leu Val Arg Gln Gln Leu Pro Glu Lys Tyr Lys Glu Ile Phe Phe             340                 345                 350 Asp Gln Ser Lys Asn Gly Tyr Ala Gly Tyr Ile Asp Gly Gly Ala Ser         355                 360                 365 Gln Glu Glu Phe Tyr Lys Phe Ile Lys Pro Ile Leu Glu Lys Met Asp     370                 375                 380 Gly Thr Glu Glu Leu Leu Val Lys Leu Asn Arg Glu Asp Leu Leu Arg 385                 390                 395                 400 Lys Gln Arg Thr Phe Asp Asn Gly Ser Ile Pro His Gln Ile His Leu                 405                 410                 415 Gly Glu Leu His Ala Ile Leu Arg Arg Gln Glu Asp Phe Tyr Pro Phe             420                 425                 430 Leu Lys Asp Asn Arg Glu Lys Ile Glu Lys Ile Leu Thr Phe Arg Ile         435                 440                 445 Pro Tyr Tyr Val Gly Pro Leu Ala Arg Gly Asn Ser Arg Phe Ala Trp     450                 455                 460 Met Thr Arg Lys Ser Glu Glu Thr Ile Thr Pro Trp Asn Phe Glu Glu 465                 470                 475                 480 Val Val Asp Lys Gly Ala Ser Ala Gln Ser Phe Ile Glu Arg Met Thr                 485                 490                 495 Asn Phe Asp Lys Asn Leu Pro Asn Glu Lys Val Leu Pro Lys His Ser             500                 505                 510 Leu Leu Tyr Glu Tyr Phe Thr Val Tyr Asn Glu Leu Thr Lys Val Lys         515                 520                 525 Tyr Val Thr Glu Gly Met Arg Lys Pro Ala Phe Leu Ser Gly Glu Gln     530                 535                 540 Lys Lys Ala Ile Val Asp Leu Leu Phe Lys Thr Asn Arg Lys Val Thr 545                 550                 555                 560 Val Lys Gln Leu Lys Glu Asp Tyr Phe Lys Lys Ile Glu Cys Phe Asp                 565                 570                 575 Ser Val Glu Ile Ser Gly Val Glu Asp Arg Phe Asn Ala Ser Leu Gly             580                 585                 590 Thr Tyr His Asp Leu Leu Lys Ile Ile Lys Asp Lys Asp Phe Leu Asp         595                 600                 605 Asn Glu Glu Asn Glu Asp Ile Leu Glu Asp Ile Val Leu Thr Leu Thr     610                 615                 620 Leu Phe Glu Asp Arg Glu Met Ile Glu Glu Arg Leu Lys Thr Tyr Ala 625                 630                 635                 640 His Leu Phe Asp Asp Lys Val Met Lys Gln Leu Lys Arg Arg Arg Tyr                 645                 650                 655 Thr Gly Trp Gly Arg Leu Ser Arg Lys Leu Ile Asn Gly Ile Arg Asp             660                 665                 670 Lys Gln Ser Gly Lys Thr Ile Leu Asp Phe Leu Lys Ser Asp Gly Phe         675                 680                 685 Ala Asn Arg Asn Phe Met Gln Leu Ile His Asp Asp Ser Leu Thr Phe     690                 695                 700 Lys Glu Asp Ile Gln Lys Ala Gln Val Ser Gly Gln Gly Asp Ser Leu 705                 710                 715                 720 His Glu His Ile Ala Asn Leu Ala Gly Ser Pro Ala Ile Lys Lys Gly                 725                 730                 735 Ile Leu Gln Thr Val Lys Val Val Asp Glu Leu Val Lys Val Met Gly             740                 745                 750 Arg His Lys Pro Glu Asn Ile Val Ile Glu Met Ala Arg Glu Asn Gln         755                 760                 765 Thr Thr Gln Lys Gly Gln Lys Asn Ser Arg Glu Arg Met Lys Arg Ile     770                 775                 780 Glu Glu Gly Ile Lys Glu Leu Gly Ser Gln Ile Leu Lys Glu His Pro 785                 790                 795                 800 Val Glu Asn Thr Gln Leu Gln Asn Glu Lys Leu Tyr Leu Tyr Tyr Leu                 805                 810                 815 Gln Asn Gly Arg Asp Met Tyr Val Asp Gln Glu Leu Asp Ile Asn Arg             820                 825                 830 Leu Ser Asp Tyr Asp Val Asp His Ile Val Pro Gln Ser Phe Leu Lys         835                 840                 845 Asp Asp Ser Ile Asp Asn Lys Val Leu Thr Arg Ser Asp Lys Asn Arg     850                 855                 860 Gly Lys Ser Asp Asn Val Pro Ser Glu Glu Val Val Lys Lys Met Lys 865                 870                 875                 880 Asn Tyr Trp Arg Gln Leu Leu Asn Ala Lys Leu Ile Thr Gln Arg Lys                 885                 890                 895 Phe Asp Asn Leu Thr Lys Ala Glu Arg Gly Gly Leu Ser Glu Leu Asp             900                 905                 910 Lys Ala Gly Phe Ile Lys Arg Gln Leu Val Glu Thr Arg Gln Ile Thr         915                 920                 925 Lys His Val Ala Gln Ile Leu Asp Ser Arg Met Asn Thr Lys Tyr Asp     930                 935                 940 Glu Asn Asp Lys Leu Ile Arg Glu Val Lys Val Ile Thr Leu Lys Ser 945                 950                 955                 960 Lys Leu Val Ser Asp Phe Arg Lys Asp Phe Gln Phe Tyr Lys Val Arg                 965                 970                 975 Glu Ile Asn Asn Tyr His His Ala His Asp Ala Tyr Leu Asn Ala Val             980                 985                 990 Val Gly Thr Ala Leu Ile Lys Lys Tyr Pro Lys Leu Glu Ser Glu Phe         995                 1000                1005 Val Tyr Gly Asp Tyr Lys Val Tyr Asp Val Arg Lys Met Ile Ala Lys     1010                1015                1020 Ser Glu Gln Glu Ile Gly Lys Ala Thr Ala Lys Tyr Phe Phe Tyr Ser 1025                1030                1035                1040 Asn Ile Met Asn Phe Phe Lys Thr Glu Ile Thr Leu Ala Asn Gly Glu                 1045                1050                1055 Ile Arg Lys Arg Pro Leu Ile Glu Thr Asn Gly Glu Thr Gly Glu Ile             1060                1065                1070 Val Trp Asp Lys Gly Arg Asp Phe Ala Thr Val Arg Lys Val Leu Ser         1075                1080                1085 Met Pro Gln Val Asn Ile Val Lys Lys Thr Glu Val Gln Thr Gly Gly     1090                1095                1100 Phe Ser Lys Glu Ser Ile Leu Pro Lys Arg Asn Ser Asp Lys Leu Ile 1105                1110                1115                1120 Ala Arg Lys Lys Asp Trp Asp Pro Lys Lys Tyr Gly Gly Phe Asp Ser                 1125                1130                1135 Pro Thr Val Ala Tyr Ser Val Leu Val Val Ala Lys Val Glu Lys Gly             1140                1145                1150 Lys Ser Lys Lys Leu Lys Ser Val Lys Glu Leu Leu Gly Ile Thr Ile         1155                1160                1165 Met Glu Arg Ser Ser Phe Glu Lys Asn Pro Ile Asp Phe Leu Glu Ala     1170                1175                1180 Lys Gly Tyr Lys Glu Val Lys Lys Asp Leu Ile Ile Lys Leu Pro Lys 1185                1190                1195                1200 Tyr Ser Leu Phe Glu Leu Glu Asn Gly Arg Lys Arg Met Leu Ala Ser                 1205                1210                1215 Ala Gly Glu Leu Gln Lys Gly Asn Glu Leu Ala Leu Pro Ser Lys Tyr             1220                1225                1230 Val Asn Phe Leu Tyr Leu Ala Ser His Tyr Glu Lys Leu Lys Gly Ser         1235                1240                1245 Pro Glu Asp Asn Glu Gln Lys Gln Leu Phe Val Glu Gln His Lys His     1250                1255                1260 Tyr Leu Asp Glu Ile Ile Glu Gln Ile Ser Glu Phe Ser Lys Arg Val 1265                1270                1275                1280 Ile Leu Ala Asp Ala Asn Leu Asp Lys Val Leu Ser Ala Tyr Asn Lys                 1285                1290                1295 His Arg Asp Lys Pro Ile Arg Glu Gln Ala Glu Asn Ile Ile His Leu             1300                1305                1310 Phe Thr Leu Thr Asn Leu Gly Ala Pro Ala Ala Phe Lys Tyr Phe Asp         1315                1320                1325 Thr Thr Ile Asp Arg Lys Arg Tyr Thr Ser Thr Lys Glu Val Leu Asp     1330                1335                1340 Ala Thr Leu Ile His Gln Ser Ile Thr Gly Leu Tyr Glu Thr Arg Ile 1345                1350                1355                1360 Asp Leu Ser Gln Leu Gly Gly Asp                 1365

In embodiments, the Cas9 molecule is a S. pyogenes Cas9 variant of SEQ ID NO: 6611 that includes one or more mutations to positively charged amino acids (e.g., lysine, arginine or histidine) that introduce an uncharged or nonpolar amino acid, e.g., alanine, at said position. In embodiments, the mutation is to one or more positively charged amino acids in the nt-groove of Cas9. In embodiments, the Cas9 molecule is a S. pyogenes Cas9 variant of SEQ ID NO: 6611 that includes a mutation at position 855 of SEQ ID NO: 6611, for example a mutation to an uncharged amino acid, e.g., alanine, at position 855 of SEQ ID NO: 6611. In embodiments, the Cas9 molecule has a mutation only at position 855 of SEQ ID NO: 6611, relative to SEQ ID NO: 6611, e.g., to an uncharged amino acid, e.g., alanine. In embodiments, the Cas9 molecule is a S. pyogenes Cas9 variant of SEQ ID NO: 6611 that includes a mutation at position 810, a mutation at position 1003, and/or a mutation at position 1060 of SEQ ID NO: 6611, for example a mutation to alanine at position 810, position 1003, and/or position 1060 of SEQ ID NO: 6611. In embodiments, the Cas9 molecule has a mutation only at position 810, position 1003, and position 1060 of SEQ ID NO: 6611, relative to SEQ ID NO: 6611, e.g., where each mutation is to an uncharged amino acid, for example, alanine. In embodiments, the Cas9 molecule is a S. pyogenes Cas9 variant of SEQ ID NO: 6611 that includes a mutation at position 848, a mutation at position 1003, and/or a mutation at position 1060 of SEQ ID NO: 6611, for example a mutation to alanine at position 848, position 1003, and/or position 1060 of SEQ ID NO: 6611. In embodiments, the Cas9 molecule has a mutation only at position 848, position 1003, and position 1060 of SEQ ID NO: 6611, relative to SEQ ID NO: 6611, e.g., where each mutation is to an uncharged amino acid, for example, alanine. In embodiments, the Cas9 molecule is a Cas9 molecule as described in Slaymaker et al., Science Express, available online Dec. 1, 2015 at Science DOI: 10.1126/science.aad5227.

In embodiments, the Cas9 molecule is a S. pyogenes Cas9 variant of SEQ ID NO: 6611 that includes one or more mutations. In embodiments, the Cas9 variant comprises a mutation at position 80 of SEQ ID NO: 6611, e.g., includes a leucine at position 80 of SEQ ID NO: 6611 (i.e., comprises, e.g., consists of, SEQ ID NO: 6611 with a C80L mutation). In embodiments, the Cas9 variant comprises a mutation at position 574 of SEQ ID NO: 6611, e.g., includes a glutamic acid at position 574 of SEQ ID NO: 6611 (i.e., comprises, e.g., consists of, SEQ ID NO: 6611 with a C574E mutation). In embodiments, the Cas9 variant comprises a mutation at position 80 and a mutation at position 574 of SEQ ID NO: 6611, e.g., includes a leucine at position 80 of SEQ ID NO: 6611, and a glutamic acid at position 574 of SEQ ID NO: 6611 (i.e., comprises, e.g., consists of, SEQ ID NO: 6611 with a C80L mutation and a C574E mutation). Without being bound by theory, it is believed that such mutations improve the solution properties of the Cas9 molecule.

In embodiments, the Cas9 molecule is a S. pyogenes Cas9 variant of SEQ ID NO: 6611 that includes one or more mutations. In embodiments, the Cas9 variant comprises a mutation at position 147 of SEQ ID NO: 6611, e.g., includes a tyrosine at position 147 of SEQ ID NO: 6611 (i.e., comprises, e.g., consists of, SEQ ID NO: 6611 with a D147Y mutation). In embodiments, the Cas9 variant comprises a mutation at position 411 of SEQ ID NO: 6611, e.g., includes a threonine at position 411 of SEQ ID NO: 6611 (i.e., comprises, e.g., consists of, SEQ ID NO: 6611 with a P411T mutation). In embodiments, the Cas9 variant comprises a mutation at position 147 and a mutation at position 411 of SEQ ID NO: 6611, e.g., includes a tyrosine at position 147 of SEQ ID NO: 6611, and a threonine at position 411 of SEQ ID NO: 6611 (i.e., comprises, e.g., consists of, SEQ ID NO: 6611 with a D147Y mutation and a P411T mutation). Without being bound by theory, it is believed that such mutations improve the targeting efficiency of the Cas9 molecule, e.g., in yeast.

In embodiments, the Cas9 molecule is a S. pyogenes Cas9 variant of SEQ ID NO: 6611 that includes one or more mutations. In embodiments, the Cas9 variant comprises a mutation at position 1135 of SEQ ID NO: 6611, e.g., includes a glutamic acid at position 1135 of SEQ ID NO: 6611 (i.e., comprises, e.g., consists of, SEQ ID NO: 6611 with a D1135E mutation). Without being bound by theory, it is believed that such mutations improve the selectivity of the Cas9 molecule for the NGG PAM sequence versus the NAG PAM sequence.

In embodiments, the Cas9 molecule is a S. pyogenes Cas9 variant of SEQ ID NO: 6611 that includes one or more mutations that introduce an uncharged or nonpolar amino acid, e.g., alanine, at certain positions. In embodiments, the Cas9 molecule is a S. pyogenes Cas9 variant of SEQ ID NO: 6611 that includes a mutation at position 497, a mutation at position 661, a mutation at position 695 and/or a mutation at position 926 of SEQ ID NO: 6611, for example a mutation to alanine at position 497, position 661, position 695 and/or position 926 of SEQ ID NO: 6611. In embodiments, the Cas9 molecule has a mutation only at position 497, position 661, position 695, and position 926 of SEQ ID NO: 6611, relative to SEQ ID NO: 6611, e.g., where each mutation is to an uncharged amino acid, for example, alanine Without being bound by theory, it is believed that such mutations reduce the cutting by the Cas9 molecule at off-target sites

It will be understood that the mutations described herein to the Cas9 molecule may be combined, and may be combined with any of the fusions or other modifications described herein, and the Cas9 molecule tested in the assays described herein.

Various types of Cas molecules can be used to practice the inventions disclosed herein. In some embodiments, Cas molecules of Type II Cas systems are used. In other embodiments, Cas molecules of other Cas systems are used. For example, Type I or Type III Cas molecules may be used. Exemplary Cas molecules (and Cas systems) are described, e.g., in Haft et ai, PLoS COMPUTATIONAL BIOLOGY 2005, 1(6): e60 and Makarova et al, NATURE REVIEW MICROBIOLOGY 2011, 9:467-477, the contents of both references are incorporated herein by reference in their entirety.

In an embodiment, the Cas9 molecule comprises one or more of the following activities: a nickase activity; a double stranded cleavage activity (e.g., an endonuclease and/or exonuclease activity); a helicase activity; or the ability, together with a gRNA molecule, to localize to a target nucleic acid.

Altered Cas9 Molecules

Naturally occurring Cas9 molecules possess a number of properties, including: nickase activity, nuclease activity (e.g., endonuclease and/or exonuclease activity); helicase activity; the ability to associate functionally with a gRNA molecule; and the ability to target (or localize to) a site on a nucleic acid (e.g., PAM recognition and specificity). In an embodiment, a Cas9 molecules can include all or a subset of these properties. In typical embodiments, Cas9 molecules have the ability to interact with a gRNA molecule and, in concert with the gRNA molecule, localize to a site in a nucleic acid. Other activities, e.g., PAM specificity, cleavage activity, or helicase activity can vary more widely in Cas9 molecules.

Cas9 molecules with desired properties can be made in a number of ways, e.g., by alteration of a parental, e.g., naturally occurring Cas9 molecules to provide an altered Cas9 molecule having a desired property. For example, one or more mutations or differences relative to a parental Cas9 molecule can be introduced. Such mutations and differences comprise: substitutions (e.g., conservative substitutions or substitutions of non-essential amino acids); insertions; or deletions. In an embodiment, a Cas9 molecule can comprises one or more mutations or differences, e.g., at least 1, 2, 3, 4, 5, 10, 15, 20, 30, 40 or 50 mutations but less than 200, 100, or 80 mutations relative to a reference Cas9 molecule.

In an embodiment, a mutation or mutations do not have a substantial effect on a Cas9 activity, e.g. a Cas9 activity described herein. In an embodiment, a mutation or mutations have a substantial effect on a Cas9 activity, e.g. a Cas9 activity described herein. In an embodiment, exemplary activities comprise one or more of PAM specificity, cleavage activity, and helicase activity. A mutation(s) can be present, e.g., in: one or more RuvC-like domain, e.g., an N-terminal RuvC-like domain; an HNH-like domain; a region outside the RuvC-like domains and the HNH-like domain. In some embodiments, a mutation(s) is present in an N-terminal RuvC-like domain. In some embodiments, a mutation(s) is present in an HNH-like domain. In some embodiments, mutations are present in both an N-terminal RuvC-like domain and an HNH-like domain.

Whether or not a particular sequence, e.g., a substitution, may affect one or more activity, such as targeting activity, cleavage activity, etc, can be evaluated or predicted, e.g., by evaluating whether the mutation is conservative or by the method described in Section III. In an embodiment, a “non-essential” amino acid residue, as used in the context of a Cas9 molecule, is a residue that can be altered from the wild-type sequence of a Cas9 molecule, e.g., a naturally occurring Cas9 molecule, e.g., an active Cas9 molecule, without abolishing or more preferably, without substantially altering a Cas9 activity (e.g., cleavage activity), whereas changing an “essential” amino acid residue results in a substantial loss of activity (e.g., cleavage activity).

Cas9 Molecules with Altered PAM Recognition or No PAM Recognition

Naturally occurring Cas9 molecules can recognize specific PAM sequences, for example the PAM recognition sequences described above for S. pyogenes, S. thermophilus, S. mutans, S. aureus and N. meningitidis.

In an embodiment, a Cas9 molecule has the same PAM specificities as a naturally occurring Cas9 molecule. In other embodiments, a Cas9 molecule has a PAM specificity not associated with a naturally occurring Cas9 molecule, or a PAM specificity not associated with the naturally occurring Cas9 molecule to which it has the closest sequence homology. For example, a naturally occurring Cas9 molecule can be altered, e.g., to alter PAM recognition, e.g., to alter the PAM sequence that the Cas9 molecule recognizes to decrease off target sites and/or improve specificity; or eliminate a PAM recognition requirement. In an embodiment, a Cas9 molecule can be altered, e.g., to increase length of PAM recognition sequence and/or improve Cas9 specificity to high level of identity to decrease off target sites and increase specificity. In an embodiment, the length of the PAM recognition sequence is at least 4, 5, 6, 7, 8, 9, 10 or 15 amino acids in length. Cas9 molecules that recognize different PAM sequences and/or have reduced off-target activity can be generated using directed evolution. Exemplary methods and systems that can be used for directed evolution of Cas9 molecules are described, e.g., in Esvelt el al, Nature 2011, 472(7344): 499-503. Candidate Cas9 molecules can be evaluated, e.g., by methods described herein.

Non-Cleaving and Modified-Cleavage Cas9 Molecules

In an embodiment, a Cas9 molecule comprises a cleavage property that differs from naturally occurring Cas9 molecules, e.g., that differs from the naturally occurring Cas9 molecule having the closest homology. For example, a Cas9 molecule can differ from naturally occurring Cas9 molecules, e.g., a Cas9 molecule of S. pyogenes, as follows: its ability to modulate, e.g., decreased or increased, cleavage of a double stranded break (endonuclease and/or exonuclease activity), e.g., as compared to a naturally occurring Cas9 molecule (e.g., a Cas9 molecule of S. pyogenes); its ability to modulate, e.g., decreased or increased, cleavage of a single strand of a nucleic acid, e.g., a non-complimentary strand of a nucleic acid molecule or a complementary strand of a nucleic acid molecule (nickase activity), e.g., as compared to a naturally occurring Cas9 molecule (e.g., a Cas9 molecule of S. pyogenes); or the ability to cleave a nucleic acid molecule, e.g., a double stranded or single stranded nucleic acid molecule, can be eliminated.

Modified Cleavage Active Cas9 Molecules

In an embodiment, an active Cas9 molecule comprises one or more of the following activities: cleavage activity associated with an N-terminal RuvC-like domain; cleavage activity associated with an HNH-like domain; cleavage activity associated with an HNH domain and cleavage activity associated with an N-terminal RuvC-like domain.

In an embodiment, the Cas9 molecule is a Cas9 nickase, e.g., cleaves only a single strand of DNA. In an embodiment, the Cas9 nickase includes a mutation at position 10 and/or a mutation at position 840 of SEQ ID NO: 6611, e.g., comprises a D10A and/or H840A mutation to SEQ ID NO: 6611.

Non-Cleaving Inactive Cas9 Molecules

In an embodiment, the altered Cas9 molecule is an inactive Cas9 molecule which does not cleave a nucleic acid molecule (either double stranded or single stranded nucleic acid molecules) or cleaves a nucleic acid molecule with significantly less efficiency, e.g., less than 20, 10, 5, 1 or 0.1% of the cleavage activity of a reference Cas9 molecule, e.g., as measured by an assay described herein. The reference Cas9 molecule can by a naturally occurring unmodified Cas9 molecule, e.g., a naturally occurring Cas9 molecule such as a Cas9 molecule of S. pyogenes, S. thermophilus, S. aureus or N. meningitidis. In an embodiment, the reference Cas9 molecule is the naturally occurring Cas9 molecule having the closest sequence identity or homology. In an embodiment, the inactive Cas9 molecule lacks substantial cleavage activity associated with an N-terminal RuvC-like domain and cleavage activity associated with an HNH-like domain.

In an embodiment, the Cas9 molecule is dCas9. Tsai et al. (2014), Nat. Biotech. 32:569-577.

A catalytically inactive Cas9 molecule may be fused with a transcription repressor. An inactive Cas9 fusion protein complexes with a gRNA and localizes to a DNA sequence specified by gRNA's targeting domain, but, unlike an active Cas9, it will not cleave the target DNA. Fusion of an effector domain, such as a transcriptional repression domain, to an inactive Cas9 enables recruitment of the effector to any DNA site specified by the gRNA. Site specific targeting of a Cas9 fusion protein to a promoter region of a gene can block or affect polymerase binding to the promoter region, for example, a Cas9 fusion with a transcription factor (e.g., a transcription activator) and/or a transcriptional enhancer binding to the nucleic acid to increase or inhibit transcription activation. Alternatively, site specific targeting of a a Cas9-fusion to a transcription repressor to a promoter region of a gene can be used to decrease transcription activation.

Transcription repressors or transcription repressor domains that may be fused to an inactive Cas9 molecule can include ruppel associated box (KRAB or SKD), the Mad mSIN3 interaction domain (SID) or the ERF repressor domain (ERD).

In another embodiment, an inactive Cas9 molecule may be fused with a protein that modifies chromatin. For example, an inactive Cas9 molecule may be fused to heterochromatin protein 1 (HP1), a histone lysine methyltransferase (e.g., SUV39H 1, SUV39H2, G9A, ESET/SETDB 1, Pr-SET7/8, SUV4-20H 1,RIZ1), a histone lysine demethylates (e.g., LSD1/BHC1 10, SpLsdl/Sw, 1/Safl 10, Su(var)3-3, JMJD2A/JHDM3A, JMJD2B, JMJD2C/GASC1, JMJD2D, Rph1, JARID 1 A/RBP2, JARI DIB/PLU-I, JAR1D 1C/SMCX, JARID1 D/SMCY, Lid, Jhn2, Jmj2), a histone lysine deacetylases (e.g., HDAC1, HDAC2, HDAC3, HDAC8, Rpd3, Hos 1, Cir6, HDAC4, HDAC5, HDAC7, HDAC9, Hda1, Cir3, SIRT 1, SIRT2, Sir2, Hst 1, Hst2, Hst3, Hst4, HDAC 11) and a DNA methylases (DNMT1,DNMT2a/DMNT3b, MET1). An inactive Cas9-chomatin modifying molecule fusion protein can be used to alter chromatin status to reduce expression a target gene.

The heterologous sequence (e.g., the transcription repressor domain) may be fused to the N- or C-terminus of the inactive Cas9 protein. In an alternative embodiment, the heterologous sequence (e.g., the transcription repressor domain) may be fused to an internal portion (i.e., a portion other than the N-terminus or C-terminus) of the inactive Cas9 protein.

The ability of a Cas9 molecule/gRNA molecule complex to bind to and cleave a target nucleic acid can be evaluated, e.g., by the methods described herein in Section III. The activity of a Cas9 molecule, e.g., either an active Cas9 or a inactive Cas9, alone or in a complex with a gRNA molecule may also be evaluated by methods well-known in the art, including, gene expression assays and chromatin-based assays, e.g., chromatin immunoprecipitation (ChiP) and chromatin in vivo assay (CiA).

Other Cas9 Molecule Fusions

In embodiments, the Cas9 molecule, e.g, a Cas9 of S. pyogenes, may additionally comprise one or more amino acid sequences that confer additional activity.

In some aspects, the Cas9 molecule may comprise one or more nuclear localization sequences (NLSs), such as at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more NLSs. In some embodiments, the Cas9 molecule comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more NLSs at or near the amino-terminus, at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more NLSs at or near the carboxy-terminus, or a combination of these (e.g. one or more NLS at the amino-terminus and one or more NLS at the carboxy terminus). When more than one NLS is present, each may be selected independently of the others, such that a single NLS may be present in more than one copy and/or in combination with one or more other NLSs present in one or more copies. In some embodiments, an NLS is considered near the N- or C-terminus when the nearest amino acid of the NLS is within about 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 40, 50, or more amino acids along the polypeptide chain from the N- or C-terminus. Typically, an NLS consists of one or more short sequences of positively charged lysines or arginines exposed on the protein surface, but other types of NLS are known. Non-limiting examples of NLSs include an NLS sequence comprising or derived from: the NLS of the SV40 virus large T-antigen, having the amino acid sequence PKKKRKV (SEQ ID NO: 6612); the NLS from nucleoplasmin (e.g. the nucleoplasmin bipartite NLS with the sequence KRPAATKKAGQAKKKK (SEQ ID NO: 6613); the c-myc NLS having the amino acid sequence PAAKRVKLD (SEQ ID NO: 6614) or RQRRNELKRSP (SEQ ID NO: 6615); the hRNPA1 M9 NLS having the sequence NQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGY (SEQ ID NO: 6616); the sequence RMRIZFKNKGKDTAELRRRRVEVSVELRKAKKDEQILKRRNV (SEQ ID NO: 6617) of the IBB domain from importin-alpha; the sequences VSRKRPRP (SEQ ID NO: 6618) and PPKKARED (SEQ ID NO: 6619) of the myoma T protein; the sequence PQPKKKPL (SEQ ID NO: 6620) of human p53; the sequence SALIKKKKKMAP (SEQ ID NO: 6621) of mouse c-ab1 IV; the sequences DRLRR (SEQ ID NO: 6622) and PKQKKRK (SEQ ID NO: 6623) of the influenza virus NS1; the sequence RKLKKKIKKL (SEQ ID NO: 6624) of the Hepatitis virus delta antigen; the sequence REKKKFLKRR (SEQ ID NO: 6625) of the mouse Mxl protein; the sequence KRKGDEVDGVDEVAKKKSKK (SEQ ID NO: 6626) of the human poly(ADP-ribose) polymerase; and the sequence RKCLQAGMNLEARKTKK (SEQ ID NO: 6627) of the steroid hormone receptors (human) glucocorticoid. Other suitable NLS sequences are known in the art (e.g., Sorokin, Biochemistry (Moscow) (2007) 72:13, 1439-1457; Lange J Biol Chem. (2007) 282:8, 5101-5).

In an embodiment, the Cas9 molecule, e.g., S. pyogenes Cas9 molecule, comprises a NLS sequence of SV40, e.g., disposed N terminal to the Cas9 molecule. In an embodiment, the Cas9 molecule, e.g., S. pyogenes Cas9 molecule, comprises a NLS sequence of SV40 disposed N-terminal to the Cas9 molecule and a NLS sequence of SV40 disposed C terminal to the Cas9 molecule. In an embodiment, the Cas9 molecule, e.g., S. pyogenes Cas9 molecule, comprises a NLS sequence of SV40 disposed N-terminal to the Cas9 molecule and a NLS sequence of nucleoplasmin disposed C-terminal to the Cas9 molecule. In any of the aforementioned embodiments, the molecule may additionally comprise a tag, e.g., a His tag, e.g., a His(6) tag or His(8) tag, e.g., at the N terminus or the C terminus.

In some aspects, the Cas9 molecule may comprise one or more amino acid sequences that allow the Cas9 molecule to be specifically recognized, for example a tag. In one embodiment, the tag is a Histidine tag, e.g., a histidine tag comprising at least 3, 4, 5, 6, 7, 8, 9, 10 or more histidine amino acids. In embodiments, the histidine tag is a His6 tag (six histidines). In other embodiments, the histidine tag is a His8 tag (eight histidines). In embodiments, the histidine tag may be separated from one or more other portions of the Cas9 molecule by a linker. In embodiments, the linker is GGS. An example of such a fusion is the Cas9 molecule iProt106520.

In some aspects, the Cas9 molecule may comprise one or more amino acid sequences that are recognized by a protease (e.g., comprise a protease cleavage site). In embodiments, the cleavage site is the tobacco etch virus (TEV) cleavage site, e.g., comprises the sequence ENLYFQG (SEQ ID NO: 7810). In some aspects the protease cleavage site, e.g., the TEV cleavage site is disposed between a tag, e.g., a His tag, e.g., a His6 or His8 tag, and the remainder of the Cas9 molecule. Without being bound by theory it is believed that such introduction will allow for the use of the tag for, e.g., purification of the Cas9 molecule, and then subsequent cleavage so the tag does not interfere with the Cas9 molecule function.

In embodiments, the Cas9 molecule (e.g., a Cas9 molecule as described herein) comprises an N-terminal NLS, and a C-terminal NLS (e.g., comprises, from N- to C-terminal NLS-Cas9-NLS), e.g., wherein each NLS is an SV40 NLS (PKKKRKV (SEQ ID NO: 6612)). In embodiments, the Cas9 molecule (e.g., a Cas9 molecule as described herein) comprises an N-terminal NLS, a C-terminal NLS, and a C-terminal His6 tag (e.g., comprises, from N- to C-terminal NLS-Cas9-NLS-His tag), e.g., wherein each NLS is an SV40 NLS (PKKKRKV (SEQ ID NO: 6612)). In embodiments, the Cas9 molecule (e.g., a Cas9 molecule as described herein) comprises an N-terminal His tag (e.g., His6 tag), an N-terminal NLS, and a C-terminal NLS (e.g., comprises, from N- to C-terminal His tag-NLS-Cas9-NLS), e.g., wherein each NLS is an SV40 NLS (PKKKRKV (SEQ ID NO: 6612)). In embodiments, the Cas9 molecule (e.g., a Cas9 molecule as described herein) comprises an N-terminal NLS and a C-terminal His tag (e.g., His6 tag) (e.g., comprises from N- to C-terminal His tag-Cas9-NLS), e.g., wherein the NLS is an SV40 NLS (PKKKRKV (SEQ ID NO: 6612)). In embodiments, the Cas9 molecule (e.g., a Cas9 molecule as described herein) comprises an N-terminal NLS and a C-terminal His tag (e.g., His6 tag) (e.g., comprises from N- to C-terminal NLS-Cas9-His tag), e.g., wherein the NLS is an SV40 NLS (PKKKRKV (SEQ ID NO: 6612)). In embodiments, the Cas9 molecule (e.g., a Cas9 molecule as described herein) comprises an N-terminal His tag (e.g., His8 tag), an N-terminal cleavage domain (e.g., a tobacco etch virus (TEV) cleavage domain (e.g., comprises the sequence ENLYFQG (SEQ ID NO: 7810))), an N-terminal NLS (e.g., an SV40 NLS; SEQ ID NO: 6612), and a C-terminal NLS (e.g., an SV40 NLS; SEQ ID NO: 6612) (e.g., comprises from N- to C-terminal His tag-TEV-NLS-Cas9-NLS). In any of the aforementioned embodiments the Cas9 has the sequence of SEQ ID NO: 6611. Alternatively, in any of the aforementioned embodiments, the Cas9 has a sequence of a Cas9 variant of SEQ ID NO: 6611, e.g., as described herein. In any of the aforementioned embodiments, the Cas9 molecule comprises a linker between the His tag and another portion of the molecule, e.g., a GGS linker. Amino acid sequences of exemplary Cas9 molecules described above are provided below. “iProt” identifiers match those in FIG. 60.

iProt105026 (also referred to as iProt106154, iProt106331, iProt106545, and PID426303, depending on the preparation of the protein) (SEQ ID NO: 7821): MAPKKKRKVD KKYSIGLDIG TNSVGWAVIT DEYKVPSKKF KVLGNTDRHS IKKNLIGALL FDSGETAEAT RLKRTARRRY TRRKNRICYL QEIFSNEMAK VDDSFFHRLE ESFLVEEDKK HERHPIFGNI VDEVAYHEKY PTIYHLRKKL VDSTDKADLR LIYLALAHMI KFRGHFLIEG DLNPDNSDVD KLFIQLVQTY NQLFEENPIN ASGVDAKAIL SARLSKSRRL ENLIAQLPGE KKNGLFGNLI ALSLGLTPNF KSNFDLAEDA KLQLSKDTYD DDLDNLLAQI GDQYADLFLA AKNLSDAILL SDILRVNTEI TKAPLSASMI KRYDEHHQDL TLLKALVRQQ LPEKYKEIFF DQSKNGYAGY IDGGASQEEF YKFIKPILEK MDGTEELLVK LNREDLLRKQ RTFDNGSIPH QIHLGELHAI LRRQEDFYPF LKDNREKIEK ILTFRIPYYV GPLARGNSRF AWMTRKSEET ITPWNFEEVV DKGASAQSFI ERMTNFDKNL PNEKVLPKHS LLYEYFTVYN ELTKVKYVTE GMRKPAFLSG EQKKAIVDLL FKTNRKVTVK QLKEDYFKKI ECFDSVEISG VEDRFNASLG TYHDLLKIIK DKDFLDNEEN EDILEDIVLT LTLFEDREMI EERLKTYAHL FDDKVMKQLK RRRYTGWGRL SRKLINGIRD KQSGKTILDF LKSDGFANRN FMQLIHDDSL TFKEDIQKAQ VSGQGDSLHE HIANLAGSPA IKKGILQTVK VVDELVKVMG RHKPENIVIE MARENQTTQK GQKNSRERMK RIEEGIKELG SQILKEHPVE NTQLQNEKLY LYYLQNGRDM YVDQELDINR LSDYDVDHIV PQSFLKDDSI DNKVLTRSDK NRGKSDNVPS EEVVKKMKNY WRQLLNAKLI TQRKFDNLTK AERGGLSELD KAGFIKRQLV ETRQITKHVA QILDSRMNTK YDENDKLIRE VKVITLKSKL VSDFRKDFQF YKVREINNYH HAHDAYLNAV VGTALIKKYP KLESEFVYGD YKVYDVRKMI AKSEQEIGKA TAKYFFYSNI MNFFKTEITL ANGEIRKRPL IETNGETGEI VWDKGRDFAT VRKVLSMPQV NIVKKTEVQT GGFSKESILP KRNSDKLIAR KKDWDPKKYG GFDSPTVAYS VLVVAKVEKG KSKKLKSVKE LLGITIMERS SFEKNPIDFL EAKGYKEVKK DLIIKLPKYS LFELENGRKR MLASAGELQK GNELALPSKY VNFLYLASHY EKLKGSPEDN EQKQLFVEQH KHYLDEIIEQ ISEFSKRVIL ADANLDKVLS AYNKHRDKPI REQAENIIHL FTLTNLGAPA AFKYFDTTID RKRYTSTKEV LDATLIHQSI TGLYETRIDL SQLGGDSRAD PKKKRKVHHH HHH iProt106518 (SEQ ID NO: 7822): MAPKKKRKVD KKYSIGLDIG TNSVGWAVIT DEYKVPSKKF KVLGNTDRHS IKKNLIGALL FDSGETAEAT RLKRTARRRY TRRKNRILYL QEIFSNEMAK VDDSFFHRLE ESFLVEEDKK HERHPIFGNI VDEVAYHEKY PTIYHLRKKL VDSTDKADLR LIYLALAHMI KFRGHFLIEG DLNPDNSDVD KLFIQLVQTY NQLFEENPIN ASGVDAKAIL SARLSKSRRL ENLIAQLPGE KKNGLFGNLI ALSLGLTPNF KSNFDLAEDA KLQLSKDTYD DDLDNLLAQI GDQYADLFLA AKNLSDAILL SDILRVNTEI TKAPLSASMI KRYDEHHQDL TLLKALVRQQ LPEKYKEIFF DQSKNGYAGY IDGGASQEEF YKFIKPILEK MDGTEELLVK LNREDLLRKQ RTFDNGSIPH QIHLGELHAI LRRQEDFYPF LKDNREKIEK ILTFRIPYYV GPLARGNSRF AWMTRKSEET ITPWNFEEVV DKGASAQSFI ERMTNFDKNL PNEKVLPKHS LLYEYFTVYN ELTKVKYVTE GMRKPAFLSG EQKKAIVDLL FKTNRKVTVK QLKEDYFKKI EEFDSVEISG VEDRFNASLG TYHDLLKIIK DKDFLDNEEN EDILEDIVLT LTLFEDREMI EERLKTYAHL FDDKVMKQLK RRRYTGWGRL SRKLINGIRD KQSGKTILDF LKSDGFANRN FMQLIHDDSL TFKEDIQKAQ VSGQGDSLHE HIANLAGSPA IKKGILQTVK VVDELVKVMG RHKPENIVIE MARENQTTQK GQKNSRERMK RIEEGIKELG SQILKEHPVE NTQLQNEKLY LYYLQNGRDM YVDQELDINR LSDYDVDHIV PQSFLKDDSI DNKVLTRSDK NRGKSDNVPS EEVVKKMKNY WRQLLNAKLI TQRKFDNLTK AERGGLSELD KAGFIKRQLV ETRQITKHVA QILDSRMNTK YDENDKLIRE VKVITLKSKL VSDFRKDFQF YKVREINNYH HAHDAYLNAV VGTALIKKYP KLESEFVYGD YKVYDVRKMI AKSEQEIGKA TAKYFFYSNI MNFFKTEITL ANGEIRKRPL IETNGETGEI VWDKGRDFAT VRKVLSMPQV NIVKKTEVQT GGFSKESILP KRNSDKLIAR KKDWDPKKYG GFDSPTVAYS VLVVAKVEKG KSKKLKSVKE LLGITIMERS SFEKNPIDFL EAKGYKEVKK DLIIKLPKYS LFELENGRKR MLASAGELQK GNELALPSKY VNFLYLASHY EKLKGSPEDN EQKQLFVEQH KHYLDEIIEQ ISEFSKRVIL ADANLDKVLS AYNKHRDKPI REQAENIIHL FTLTNLGAPA AFKYFDTTID RKRYTSTKEV LDATLIHQSI TGLYETRIDL SQLGGDSRAD PKKKRKVHHH HHH iProt106519 (SEQ ID NO: 7823): MGSSHHHHHH HHENLYFQGS MDKKYSIGLD IGTNSVGWAV ITDEYKVPSK KFKVLGNTDR HSIKKNLIGA LLFDSGETAE ATRLKRTARR RYTRRKNRIC YLQEIFSNEM AKVDDSFFHR LEESFLVEED KKHERHPIFG NIVDEVAYHE KYPTIYHLRK KLVDSTDKAD LRLIYLALAH MIKFRGHFLI EGDLNPDNSD VDKLFIQLVQ TYNQLFEENP INASGVDAKA ILSARLSKSR RLENLIAQLP GEKKNGLFGN LIALSLGLTP NFKSNFDLAE DAKLQLSKDT YDDDLDNLLA QIGDQYADLF LAAKNLSDAI LLSDILRVNT EITKAPLSAS MIKRYDEHHQ DLTLLKALVR QQLPEKYKEI FFDQSKNGYA GYIDGGASQE EFYKFIKPIL EKMDGTEELL VKLNREDLLR KQRTFDNGSI PHQIHLGELH AILRRQEDFY PFLKDNREKI EKILTFRIPY YVGPLARGNS RFAWMTRKSE ETITPWNFEE VVDKGASAQS FIERMTNFDK NLPNEKVLPK HSLLYEYFTV YNELTKVKYV TEGMRKPAFL SGEQKKAIVD LLFKTNRKVT VKQLKEDYFK KIECFDSVEI SGVEDRFNAS LGTYHDLLKI IKDKDFLDNE ENEDILEDIV LTLTLFEDRE MIEERLKTYA HLFDDKVMKQ LKRRRYTGWG RLSRKLINGI RDKQSGKTIL DFLKSDGFAN RNFMQLIHDD SLTFKEDIQK AQVSGQGDSL HEHIANLAGS PAIKKGILQT VKVVDELVKV MGRHKPENIV IEMARENQTT QKGQKNSRER MKRIEEGIKE LGSQILKEHP VENTQLQNEK LYLYYLQNGR DMYVDQELDI NRLSDYDVDH IVPQSFLKDD SIDNKVLTRS DKNRGKSDNV PSEEVVKKMK NYWRQLLNAK LITQRKFDNL TKAERGGLSE LDKAGFIKRQ LVETRQITKH VAQILDSRMN TKYDENDKLI REVKVITLKS KLVSDFRKDF QFYKVREINN YHHAHDAYLN AVVGTALIKK YPKLESEFVY GDYKVYDVRK MIAKSEQEIG KATAKYFFYS NIMNFFKTEI TLANGEIRKR PLIETNGETG EIVWDKGRDF ATVRKVLSMP QVNIVKKTEV QTGGFSKESI LPKRNSDKLI ARKKDWDPKK YGGFDSPTVA YSVLVVAKVE KGKSKKLKSV KELLGITIME RSSFEKNPID FLEAKGYKEV KKDLIIKLPK YSLFELENGR KRMLASAGEL QKGNELALPS KYVNFLYLAS HYEKLKGSPE DNEQKQLFVE QHKHYLDEII EQISEFSKRV ILADANLDKV LSAYNKHRDK PIREQAENII HLFTLTNLGA PAAFKYFDTT IDRKRYTSTK EVLDATLIHQ SITGLYETRI DLSQLGGDGG GSPKKKRKV iProt106520 (SEQ ID NO: 7824): MAHHHHHHGG SPKKKRKVDK KYSIGLDIGT NSVGWAVITD EYKVPSKKFK VLGNTDRHSI KKNLIGALLF DSGETAEATR LKRTARRRYT RRKNRICYLQ EIFSNEMAKV DDSFFHRLEE SFLVEEDKKH ERHPIFGNIV DEVAYHEKYP TIYHLRKKLV DSTDKADLRL IYLALAHMIK FRGHFLIEGD LNPDNSDVDK LFIQLVQTYN QLFEENPINA SGVDAKAILS ARLSKSRRLE NLIAQLPGEK KNGLFGNLIA LSLGLTPNFK SNFDLAEDAK LQLSKDTYDD DLDNLLAQIG DQYADLFLAA KNLSDAILLS DILRVNTEIT KAPLSASMIK RYDEHHQDLT LLKALVRQQL PEKYKEIFFD QSKNGYAGYI DGGASQEEFY KFIKPILEKM DGTEELLVKL NREDLLRKQR TFDNGSIPHQ IHLGELHAIL RRQEDFYPFL KDNREKIEKI LTFRIPYYVG PLARGNSRFA WMTRKSEETI TPWNFEEVVD KGASAQSFIE RMTNFDKNLP NEKVLPKHSL LYEYFTVYNE LTKVKYVTEG MRKPAFLSGE QKKAIVDLLF KTNRKVTVKQ LKEDYFKKIE CFDSVEISGV EDRFNASLGT YHDLLKIIKD KDFLDNEENE DILEDIVLTL TLFEDREMIE ERLKTYAHLF DDKVMKQLKR RRYTGWGRLS RKLINGIRDK QSGKTILDFL KSDGFANRNF MQLIHDDSLT FKEDIQKAQV SGQGDSLHEH IANLAGSPAI KKGILQTVKV VDELVKVMGR HKPENIVIEM ARENQTTQKG QKNSRERMKR IEEGIKELGS QILKEHPVEN TQLQNEKLYL YYLQNGRDMY VDQELDINRL SDYDVDHIVP QSFLKDDSID NKVLTRSDKN RGKSDNVPSE EVVKKMKNYW RQLLNAKLIT QRKFDNLTKA ERGGLSELDK AGFIKRQLVE TRQITKHVAQ ILDSRMNTKY DENDKLIREV KVITLKSKLV SDFRKDFQFY KVREINNYHH AHDAYLNAVV GTALIKKYPK LESEFVYGDY KVYDVRKMIA KSEQEIGKAT AKYFFYSNIM NFFKTEITLA NGEIRKRPLI ETNGETGEIV WDKGRDFATV RKVLSMPQVN IVKKTEVQTG GFSKESILPK RNSDKLIARK KDWDPKKYGG FDSPTVAYSV LVVAKVEKGK SKKLKSVKEL LGITIMERSS FEKNPIDFLE AKGYKEVKKD LIIKLPKYSL FELENGRKRM LASAGELQKG NELALPSKYV NFLYLASHYE KLKGSPEDNE QKQLFVEQHK HYLDEIIEQI SEFSKRVILA DANLDKVLSA YNKHRDKPIR EQAENIIHLF TLTNLGAPAA FKYFDTTIDR KRYTSTKEVL DATLIHQSIT GLYETRIDLS QLGGDSRADP KKKRKV iProt106521 (SEQ ID NO: 7825): MAPKKKRKVD KKYSIGLDIG TNSVGWAVIT DEYKVPSKKF KVLGNTDRHS IKKNLIGALL FDSGETAEAT RLKRTARRRY TRRKNRICYL QEIFSNEMAK VDDSFFHRLE ESFLVEEDKK HERHPIFGNI VDEVAYHEKY PTIYHLRKKL VDSTDKADLR LIYLALAHMI KFRGHFLIEG DLNPDNSDVD KLFIQLVQTY NQLFEENPIN ASGVDAKAIL SARLSKSRRL ENLIAQLPGE KKNGLFGNLI ALSLGLTPNF KSNFDLAEDA KLQLSKDTYD DDLDNLLAQI GDQYADLFLA AKNLSDAILL SDILRVNTEI TKAPLSASMI KRYDEHHQDL TLLKALVRQQ LPEKYKEIFF DQSKNGYAGY IDGGASQEEF YKFIKPILEK MDGTEELLVK LNREDLLRKQ RTFDNGSIPH QIHLGELHAI LRRQEDFYPF LKDNREKIEK ILTFRIPYYV GPLARGNSRF AWMTRKSEET ITPWNFEEVV DKGASAQSFI ERMTNFDKNL PNEKVLPKHS LLYEYFTVYN ELTKVKYVTE GMRKPAFLSG EQKKAIVDLL FKTNRKVTVK QLKEDYFKKI ECFDSVEISG VEDRFNASLG TYHDLLKIIK DKDFLDNEEN EDILEDIVLT LTLFEDREMI EERLKTYAHL FDDKVMKQLK RRRYTGWGRL SRKLINGIRD KQSGKTILDF LKSDGFANRN FMQLIHDDSL TFKEDIQKAQ VSGQGDSLHE HIANLAGSPA IKKGILQTVK VVDELVKVMG RHKPENIVIE MARENQTTQK GQKNSRERMK RIEEGIKELG SQILKEHPVE NTQLQNEKLY LYYLQNGRDM YVDQELDINR LSDYDVDHIV PQSFLKDDSI DNKVLTRSDK NRGKSDNVPS EEVVKKMKNY WRQLLNAKLI TQRKFDNLTK AERGGLSELD KAGFIKRQLV ETRQITKHVA QILDSRMNTK YDENDKLIRE VKVITLKSKL VSDFRKDFQF YKVREINNYH HAHDAYLNAV VGTALIKKYP KLESEFVYGD YKVYDVRKMI AKSEQEIGKA TAKYFFYSNI MNFFKTEITL ANGEIRKRPL IETNGETGEI VWDKGRDFAT VRKVLSMPQV NIVKKTEVQT GGFSKESILP KRNSDKLIAR KKDWDPKKYG GFDSPTVAYS VLVVAKVEKG KSKKLKSVKE LLGITIMERS SFEKNPIDFL EAKGYKEVKK DLIIKLPKYS LFELENGRKR MLASAGELQK GNELALPSKY VNFLYLASHY EKLKGSPEDN EQKQLFVEQH KHYLDEIIEQ ISEFSKRVIL ADANLDKVLS AYNKHRDKPI REQAENIIHL FTLTNLGAPA AFKYFDTTID RKRYTSTKEV LDATLIHQSI TGLYETRIDL SQLGGDSRAD HHHHHH iProt106522 (SEQ ID NO: 7826): MAHHHHHHGG SDKKYSIGLD IGTNSVGWAV ITDEYKVPSK KFKVLGNTDR HSIKKNLIGA LLFDSGETAE ATRLKRTARR RYTRRKNRIC YLQEIFSNEM AKVDDSFFHR LEESFLVEED KKHERHPIFG NIVDEVAYHE KYPTIYHLRK KLVDSTDKAD LRLIYLALAH MIKFRGHFLI EGDLNPDNSD VDKLFIQLVQ TYNQLFEENP INASGVDAKA ILSARLSKSR RLENLIAQLP GEKKNGLFGN LIALSLGLTP NFKSNFDLAE DAKLQLSKDT YDDDLDNLLA QIGDQYADLF LAAKNLSDAI LLSDILRVNT EITKAPLSAS MIKRYDEHHQ DLTLLKALVR QQLPEKYKEI FFDQSKNGYA GYIDGGASQE EFYKFIKPIL EKMDGTEELL VKLNREDLLR KQRTFDNGSI PHQIHLGELH AILRRQEDFY PFLKDNREKI EKILTFRIPY YVGPLARGNS RFAWMTRKSE ETITPWNFEE VVDKGASAQS FIERMTNFDK NLPNEKVLPK HSLLYEYFTV YNELTKVKYV TEGMRKPAFL SGEQKKAIVD LLFKTNRKVT VKQLKEDYFK KIECFDSVEI SGVEDRFNAS LGTYHDLLKI IKDKDFLDNE ENEDILEDIV LTLTLFEDRE MIEERLKTYA HLFDDKVMKQ LKRRRYTGWG RLSRKLINGI RDKQSGKTIL DFLKSDGFAN RNFMQLIHDD SLTFKEDIQK AQVSGQGDSL HEHIANLAGS PAIKKGILQT VKVVDELVKV MGRHKPENIV IEMARENQTT QKGQKNSRER MKRIEEGIKE LGSQILKEHP VENTQLQNEK LYLYYLQNGR DMYVDQELDI NRLSDYDVDH IVPQSFLKDD SIDNKVLTRS DKNRGKSDNV PSEEVVKKMK NYWRQLLNAK LITQRKFDNL TKAERGGLSE LDKAGFIKRQ LVETRQITKH VAQILDSRMN TKYDENDKLI REVKVITLKS KLVSDFRKDF QFYKVREINN YHHAHDAYLN AVVGTALIKK YPKLESEFVY GDYKVYDVRK MIAKSEQEIG KATAKYFFYS NIMNFFKTEI TLANGEIRKR PLIETNGETG EIVWDKGRDF ATVRKVLSMP QVNIVKKTEV QTGGFSKESI LPKRNSDKLI ARKKDWDPKK YGGFDSPTVA YSVLVVAKVE KGKSKKLKSV KELLGITIME RSSFEKNPID FLEAKGYKEV KKDLIIKLPK YSLFELENGR KRMLASAGEL QKGNELALPS KYVNFLYLAS HYEKLKGSPE DNEQKQLFVE QHKHYLDEII EQISEFSKRV ILADANLDKV LSAYNKHRDK PIREQAENII HLFTLTNLGA PAAFKYFDTT IDRKRYTSTK EVLDATLIHQ SITGLYETRI DLSQLGGDSR ADPKKKRKV iProt106658 (SEQ ID NO: 7827): MGSSHHHHHH HHENLYFQGS MDKKYSIGLD IGTNSVGWAV ITDEYKVPSK KFKVLGNTDR HSIKKNLIGA LLFDSGETAE ATRLKRTARR RYTRRKNRIC YLQEIFSNEM AKVDDSFFHR LEESFLVEED KKHERHPIFG NIVDEVAYHE KYPTIYHLRK KLVDSTDKAD LRLIYLALAH MIKFRGHFLI EGDLNPDNSD VDKLFIQLVQ TYNQLFEENP INASGVDAKA ILSARLSKSR RLENLIAQLP GEKKNGLFGN LIALSLGLTP NFKSNFDLAE DAKLQLSKDT YDDDLDNLLA QIGDQYADLF LAAKNLSDAI LLSDILRVNT EITKAPLSAS MIKRYDEHHQ DLTLLKALVR QQLPEKYKEI FFDQSKNGYA GYIDGGASQE EFYKFIKPIL EKMDGTEELL VKLNREDLLR KQRTFDNGSI PHQIHLGELH AILRRQEDFY PFLKDNREKI EKILTFRIPY YVGPLARGNS RFAWMTRKSE ETITPWNFEE VVDKGASAQS FIERMTNFDK NLPNEKVLPK HSLLYEYFTV YNELTKVKYV TEGMRKPAFL SGEQKKAIVD LLFKTNRKVT VKQLKEDYFK KIECFDSVEI SGVEDRFNAS LGTYHDLLKI IKDKDFLDNE ENEDILEDIV LTLTLFEDRE MIEERLKTYA HLFDDKVMKQ LKRRRYTGWG RLSRKLINGI RDKQSGKTIL DFLKSDGFAN RNFMQLIHDD SLTFKEDIQK AQVSGQGDSL HEHIANLAGS PAIKKGILQT VKVVDELVKV MGRHKPENIV IEMARENQTT QKGQKNSRER MKRIEEGIKE LGSQILKEHP VENTQLQNEK LYLYYLQNGR DMYVDQELDI NRLSDYDVDH IVPQSFLKDD SIDNKVLTRS DKNRGKSDNV PSEEVVKKMK NYWRQLLNAK LITQRKFDNL TKAERGGLSE LDKAGFIKRQ LVETRQITKH VAQILDSRMN TKYDENDKLI REVKVITLKS KLVSDFRKDF QFYKVREINN YHHAHDAYLN AVVGTALIKK YPKLESEFVY GDYKVYDVRK MIAKSEQEIG KATAKYFFYS NIMNFFKTEI TLANGEIRKR PLIETNGETG EIVWDKGRDF ATVRKVLSMP QVNIVKKTEV QTGGFSKESI LPKRNSDKLI ARKKDWDPKK YGGFDSPTVA YSVLVVAKVE KGKSKKLKSV KELLGITIME RSSFEKNPID FLEAKGYKEV KKDLIIKLPK YSLFELENGR KRMLASAGEL QKGNELALPS KYVNFLYLAS HYEKLKGSPE DNEQKQLFVE QHKHYLDEII EQISEFSKRV ILADANLDKV LSAYNKHRDK PIREQAENII HLFTLTNLGA PAAFKYFDTT IDRKRYTSTK EVLDATLIHQ SITGLYETRI DLSQLGGDGG GSPKKKRKV iProt106745 (SEQ ID NO: 7828): MAPKKKRKVD KKYSIGLDIG TNSVGWAVIT DEYKVPSKKF KVLGNTDRHS IKKNLIGALL FDSGETAEAT RLKRTARRRY TRRKNRICYL QEIFSNEMAK VDDSFFHRLE ESFLVEEDKK HERHPIFGNI VDEVAYHEKY PTIYHLRKKL VDSTDKADLR LIYLALAHMI KFRGHFLIEG DLNPDNSDVD KLFIQLVQTY NQLFEENPIN ASGVDAKAIL SARLSKSRRL ENLIAQLPGE KKNGLFGNLI ALSLGLTPNF KSNFDLAEDA KLQLSKDTYD DDLDNLLAQI GDQYADLFLA AKNLSDAILL SDILRVNTEI TKAPLSASMI KRYDEHHQDL TLLKALVRQQ LPEKYKEIFF DQSKNGYAGY IDGGASQEEF YKFIKPILEK MDGTEELLVK LNREDLLRKQ RTFDNGSIPH QIHLGELHAI LRRQEDFYPF LKDNREKIEK ILTFRIPYYV GPLARGNSRF AWMTRKSEET ITPWNFEEVV DKGASAQSFI ERMTNFDKNL PNEKVLPKHS LLYEYFTVYN ELTKVKYVTE GMRKPAFLSG EQKKAIVDLL FKTNRKVTVK QLKEDYFKKI ECFDSVEISG VEDRFNASLG TYHDLLKIIK DKDFLDNEEN EDILEDIVLT LTLFEDREMI EERLKTYAHL FDDKVMKQLK RRRYTGWGRL SRKLINGIRD KQSGKTILDF LKSDGFANRN FMQLIHDDSL TFKEDIQKAQ VSGQGDSLHE HIANLAGSPA IKKGILQTVK VVDELVKVMG RHKPENIVIE MARENQTTQK GQKNSRERMK RIEEGIKELG SQILKEHPVE NTQLQNEKLY LYYLQNGRDM YVDQELDINR LSDYDVDHIV PQSFLKDDSI DNAVLTRSDK NRGKSDNVPS EEVVKKMKNY WRQLLNAKLI TQRKFDNLTK AERGGLSELD KAGFIKRQLV ETRQITKHVA QILDSRMNTK YDENDKLIRE VKVITLKSKL VSDFRKDFQF YKVREINNYH HAHDAYLNAV VGTALIKKYP KLESEFVYGD YKVYDVRKMI AKSEQEIGKA TAKYFFYSNI MNFFKTEITL ANGEIRKRPL IETNGETGEI VWDKGRDFAT VRKVLSMPQV NIVKKTEVQT GGFSKESILP KRNSDKLIAR KKDWDPKKYG GFDSPTVAYS VLVVAKVEKG KSKKLKSVKE LLGITIMERS SFEKNPIDFL EAKGYKEVKK DLIIKLPKYS LFELENGRKR MLASAGELQK GNELALPSKY VNFLYLASHY EKLKGSPEDN EQKQLFVEQH KHYLDEIIEQ ISEFSKRVIL ADANLDKVLS AYNKHRDKPI REQAENIIHL FTLTNLGAPA AFKYFDTTID RKRYTSTKEV LDATLIHQSI TGLYETRIDL SQLGGDSRAD PKKKRKVHHH HHH iProt106746 (SEQ ID NO: 7829): MAPKKKRKVD KKYSIGLDIG TNSVGWAVIT DEYKVPSKKF KVLGNTDRHS IKKNLIGALL FDSGETAEAT RLKRTARRRY TRRKNRICYL QEIFSNEMAK VDDSFFHRLE ESFLVEEDKK HERHPIFGNI VDEVAYHEKY PTIYHLRKKL VDSTDKADLR LIYLALAHMI KFRGHFLIEG DLNPDNSDVD KLFIQLVQTY NQLFEENPIN ASGVDAKAIL SARLSKSRRL ENLIAQLPGE KKNGLFGNLI ALSLGLTPNF KSNFDLAEDA KLQLSKDTYD DDLDNLLAQI GDQYADLFLA AKNLSDAILL SDILRVNTEI TKAPLSASMI KRYDEHHQDL TLLKALVRQQ LPEKYKEIFF DQSKNGYAGY IDGGASQEEF YKFIKPILEK MDGTEELLVK LNREDLLRKQ RTFDNGSIPH QIHLGELHAI LRRQEDFYPF LKDNREKIEK ILTFRIPYYV GPLARGNSRF AWMTRKSEET ITPWNFEEVV DKGASAQSFI ERMTNFDKNL PNEKVLPKHS LLYEYFTVYN ELTKVKYVTE GMRKPAFLSG EQKKAIVDLL FKTNRKVTVK QLKEDYFKKI ECFDSVEISG VEDRFNASLG TYHDLLKIIK DKDFLDNEEN EDILEDIVLT LTLFEDREMI EERLKTYAHL FDDKVMKQLK RRRYTGWGRL SRKLINGIRD KQSGKTILDF LKSDGFANRN FMQLIHDDSL TFKEDIQKAQ VSGQGDSLHE HIANLAGSPA IKKGILQTVK VVDELVKVMG RHKPENIVIE MARENQTTQK GQKNSRERMK RIEEGIKELG SQILKEHPVE NTQLQNEALY LYYLQNGRDM YVDQELDINR LSDYDVDHIV PQSFLKDDSI DNKVLTRSDK NRGKSDNVPS EEVVKKMKNY WRQLLNAKLI TQRKFDNLTK AERGGLSELD KAGFIKRQLV ETRQITKHVA QILDSRMNTK YDENDKLIRE VKVITLKSKL VSDFRKDFQF YKVREINNYH HAHDAYLNAV VGTALIKKYP ALESEFVYGD YKVYDVRKMI AKSEQEIGKA TAKYFFYSNI MNFFKTEITL ANGEIRKAPL IETNGETGEI VWDKGRDFAT VRKVLSMPQV NIVKKTEVQT GGFSKESILP KRNSDKLIAR KKDWDPKKYG GFDSPTVAYS VLVVAKVEKG KSKKLKSVKE LLGITIMERS SFEKNPIDFL EAKGYKEVKK DLIIKLPKYS LFELENGRKR MLASAGELQK GNELALPSKY VNFLYLASHY EKLKGSPEDN EQKQLFVEQH KHYLDEIIEQ ISEFSKRVIL ADANLDKVLS AYNKHRDKPI REQAENIIHL FTLTNLGAPA AFKYFDTTID RKRYTSTKEV LDATLIHQSI TGLYETRIDL SQLGGDSRAD PKKKRKVHHH HHH iProt106747 (SEQ ID NO: 7830): MAPKKKRKVD KKYSIGLDIG TNSVGWAVIT DEYKVPSKKF KVLGNTDRHS IKKNLIGALL FDSGETAEAT RLKRTARRRY TRRKNRICYL QEIFSNEMAK VDDSFFHRLE ESFLVEEDKK HERHPIFGNI VDEVAYHEKY PTIYHLRKKL VDSTDKADLR LIYLALAHMI KFRGHFLIEG DLNPDNSDVD KLFIQLVQTY NQLFEENPIN ASGVDAKAIL SARLSKSRRL ENLIAQLPGE KKNGLFGNLI ALSLGLTPNF KSNFDLAEDA KLQLSKDTYD DDLDNLLAQI GDQYADLFLA AKNLSDAILL SDILRVNTEI TKAPLSASMI KRYDEHHQDL TLLKALVRQQ LPEKYKEIFF DQSKNGYAGY IDGGASQEEF YKFIKPILEK MDGTEELLVK LNREDLLRKQ RTFDNGSIPH QIHLGELHAI LRRQEDFYPF LKDNREKIEK ILTFRIPYYV GPLARGNSRF AWMTRKSEET ITPWNFEEVV DKGASAQSFI ERMTNFDKNL PNEKVLPKHS LLYEYFTVYN ELTKVKYVTE GMRKPAFLSG EQKKAIVDLL FKTNRKVTVK QLKEDYFKKI ECFDSVEISG VEDRFNASLG TYHDLLKIIK DKDFLDNEEN EDILEDIVLT LTLFEDREMI EERLKTYAHL FDDKVMKQLK RRRYTGWGRL SRKLINGIRD KQSGKTILDF LKSDGFANRN FMQLIHDDSL TFKEDIQKAQ VSGQGDSLHE HIANLAGSPA IKKGILQTVK VVDELVKVMG RHKPENIVIE MARENQTTQK GQKNSRERMK RIEEGIKELG SQILKEHPVE NTQLQNEKLY LYYLQNGRDM YVDQELDINR LSDYDVDHIV PQSFLADDSI DNKVLTRSDK NRGKSDNVPS EEVVKKMKNY WRQLLNAKLI TQRKFDNLTK AERGGLSELD KAGFIKRQLV ETRQITKHVA QILDSRMNTK YDENDKLIRE VKVITLKSKL VSDFRKDFQF YKVREINNYH HAHDAYLNAV VGTALIKKYP ALESEFVYGD YKVYDVRKMI AKSEQEIGKA TAKYFFYSNI MNFFKTEITL ANGEIRKAPL IETNGETGEI VWDKGRDFAT VRKVLSMPQV NIVKKTEVQT GGFSKESILP KRNSDKLIAR KKDWDPKKYG GFDSPTVAYS VLVVAKVEKG KSKKLKSVKE LLGITIMERS SFEKNPIDFL EAKGYKEVKK DLIIKLPKYS LFELENGRKR MLASAGELQK GNELALPSKY VNFLYLASHY EKLKGSPEDN EQKQLFVEQH KHYLDEIIEQ ISEFSKRVIL ADANLDKVLS AYNKHRDKPI REQAENIIHL FTLTNLGAPA AFKYFDTTID RKRYTSTKEV LDATLIHQSI TGLYETRIDL SQLGGDSRAD PKKKRKVHHH HHH iProt106884 (SEQ ID NO: 7831): MAPKKKRKVD KKYSIGLDIG TNSVGWAVIT DEYKVPSKKF KVLGNTDRHS IKKNLIGALL FDSGETAEAT RLKRTARRRY TRRKNRICYL QEIFSNEMAK VDDSFFHRLE ESFLVEEDKK HERHPIFGNI VDEVAYHEKY PTIYHLRKKL VDSTDKADLR LIYLALAHMI KFRGHFLIEG DLNPDNSDVD KLFIQLVQTY NQLFEENPIN ASGVDAKAIL SARLSKSRRL ENLIAQLPGE KKNGLFGNLI ALSLGLTPNF KSNFDLAEDA KLQLSKDTYD DDLDNLLAQI GDQYADLFLA AKNLSDAILL SDILRVNTEI TKAPLSASMI KRYDEHHQDL TLLKALVRQQ LPEKYKEIFF DQSKNGYAGY IDGGASQEEF YKFIKPILEK MDGTEELLVK LNREDLLRKQ RTFDNGSIPH QIHLGELHAI LRRQEDFYPF LKDNREKIEK ILTFRIPYYV GPLARGNSRF AWMTRKSEET ITPWNFEEVV DKGASAQSFI ERMTAFDKNL PNEKVLPKHS LLYEYFTVYN ELTKVKYVTE GMRKPAFLSG EQKKAIVDLL FKTNRKVTVK QLKEDYFKKI ECFDSVEISG VEDRFNASLG TYHDLLKIIK DKDFLDNEEN EDILEDIVLT LTLFEDREMI EERLKTYAHL FDDKVMKQLK RRRYTGWGAL SRKLINGIRD KQSGKTILDF LKSDGFANRN FMALIHDDSL TFKEDIQKAQ VSGQGDSLHE HIANLAGSPA IKKGILQTVK VVDELVKVMG RHKPENIVIE MARENQTTQK GQKNSRERMK RIEEGIKELG SQILKEHPVE NTQLQNEKLY LYYLQNGRDM YVDQELDINR LSDYDVDHIV PQSFLKDDSI DNKVLTRSDK NRGKSDNVPS EEVVKKMKNY WRQLLNAKLI TQRKFDNLTK AERGGLSELD KAGFIKRQLV ETRAITKHVA QILDSRMNTK YDENDKLIRE VKVITLKSKL VSDFRKDFQF YKVREINNYH HAHDAYLNAV VGTALIKKYP KLESEFVYGD YKVYDVRKMI AKSEQEIGKA TAKYFFYSNI MNFFKTEITL ANGEIRKRPL IETNGETGEI VWDKGRDFAT VRKVLSMPQV NIVKKTEVQT GGFSKESILP KRNSDKLIAR KKDWDPKKYG GFDSPTVAYS VLVVAKVEKG KSKKLKSVKE LLGITIMERS SFEKNPIDFL EAKGYKEVKK DLIIKLPKYS LFELENGRKR MLASAGELQK GNELALPSKY VNFLYLASHY EKLKGSPEDN EQKQLFVEQH KHYLDEIIEQ ISEFSKRVIL ADANLDKVLS AYNKHRDKPI REQAENIIHL FTLTNLGAPA AFKYFDTTID RKRYTSTKEV LDATLIHQSI TGLYETRIDL SQLGGDSRAD PKKKRKVHHH HHH

Nucleic Acids Encoding Cas9 Molecules

Nucleic acids encoding the Cas9 molecules, e.g., an active Cas9 molecule or an inactive Cas9 molecule are provided herein.

Exemplary nucleic acids encoding Cas9 molecules are described in Cong et al, SCIENCE 2013, 399(6121):819-823; Wang et al, CELL 2013, 153(4):910-918; Mali et al., SCIENCE 2013, 399(6121):823-826; Jinek et al, SCIENCE 2012, 337(6096):816-821.

In an embodiment, a nucleic acid encoding a Cas9 molecule can be a synthetic nucleic acid sequence. For example, the synthetic nucleic acid molecule can be chemically modified, e.g., as described in Section XIII. In an embodiment, the Cas9 mRNA has one or more of, e.g., all of the following properties: it is capped, polyadenylated, substituted with 5-methylcytidine and/or pseudouridine.

In addition or alternatively, the synthetic nucleic acid sequence can be codon optimized, e.g., at least one non-common codon or less-common codon has been replaced by a common codon. For example, the synthetic nucleic acid can direct the synthesis of an optimized messenger mRNA, e.g., optimized for expression in a mammalian expression system, e.g., described herein.

Provided below is an exemplary codon optimized nucleic acid sequence encoding a Cas9 molecule of S. pyogenes.

(SEQ ID NO: 6628) atggataaaa agtacagcat cgggctggac atcggtacaa actcagtggg gtgggccgtg 60 attacggacg agtacaaggt accctccaaa aaatttaaag tgctgggtaa cacggacaga 120 cactctataa agaaaaatct tattggagcc ttgctgttcg actcaggcga gacagccgaa 180 gccacaaggt tgaagcggac cgccaggagg cggtatacca ggagaaagaa ccgcatatgc 240 tacctgcaag aaatcttcag taacgagatg gcaaaggttg acgatagctt tttccatcgc 300 ctggaagaat cctttcttgt tgaggaagac aagaagcacg aacggcaccc catctttggc 360 aatattgtcg acgaagtggc atatcacgaa aagtacccga ctatctacca cctcaggaag 420 aagctggtgg actctaccga taaggcggac ctcagactta tttatttggc actcgcccac 480 atgattaaat ttagaggaca tttcttgatc gagggcgacc tgaacccgga caacagtgac 540 gtcgataagc tgttcatcca acttgtgcag acctacaatc aactgttcga agaaaaccct 600 ataaatgctt caggagtcga cgctaaagca atcctgtccg cgcgcctctc aaaatctaga 660 agacttgaga atctgattgc tcagttgccc ggggaaaaga aaaatggatt gtttggcaac 720 ctgatcgccc tcagtctcgg actgacccca aatttcaaaa gtaacttcga cctggccgaa 780 gacgctaagc tccagctgtc caaggacaca tacgatgacg acctcgacaa tctgctggcc 840 cagattgggg atcagtacgc cgatctcttt ttggcagcaa agaacctgtc cgacgccatc 900 ctgttgagcg atatcttgag agtgaacacc gaaattacta aagcacccct tagcgcatct 960 atgatcaagc ggtacgacga gcatcatcag gatctgaccc tgctgaaggc tcttgtgagg 1020 caacagctcc ccgaaaaata caaggaaatc ttctttgacc agagcaaaaa cggctacgct 1080 ggctatatag atggtggggc cagtcaggag gaattctata aattcatcaa gcccattctc 1140 gagaaaatgg acggcacaga ggagttgctg gtcaaactta acagggagga cctgctgcgg 1200 aagcagcgga cctttgacaa cgggtctatc ccccaccaga ttcatctggg cgaactgcac 1260 gcaatcctga ggaggcagga ggatttttat ccttttctta aagataaccg cgagaaaata 1320 gaaaagattc ttacattcag gatcccgtac tacgtgggac ctctcgcccg gggcaattca 1380 cggtttgcct ggatgacaag gaagtcagag gagactatta caccttggaa cttcgaagaa 1440 gtggtggaca agggtgcatc tgcccagtct ttcatcgagc ggatgacaaa ttttgacaag 1500 aacctcccta atgagaaggt gctgcccaaa cattctctgc tctacgagta ctttaccgtc 1560 tacaatgaac tgactaaagt caagtacgtc accgagggaa tgaggaagcc ggcattcctt 1620 agtggagaac agaagaaggc gattgtagac ctgttgttca agaccaacag gaaggtgact 1680 gtgaagcaac ttaaagaaga ctactttaag aagatcgaat gttttgacag tgtggaaatt 1740 tcaggggttg aagaccgctt caatgcgtca ttggggactt accatgatct tctcaagatc 1800 ataaaggaca aagacttcct ggacaacgaa gaaaatgagg atattctcga agacatcgtc 1860 ctcaccctga ccctgttcga agacagggaa atgatagaag agcgcttgaa aacctatgcc 1920 cacctcttcg acgataaagt tatgaagcag ctgaagcgca ggagatacac aggatgggga 1980 agattgtcaa ggaagctgat caatggaatt agggataaac agagtggcaa gaccatactg 2040 gatttcctca aatctgatgg cttcgccaat aggaacttca tgcaactgat tcacgatgac 2100 tctcttacct tcaaggagga cattcaaaag gctcaggtga gcgggcaggg agactccctt 2160 catgaacaca tcgcgaattt ggcaggttcc cccgctatta aaaagggcat ccttcaaact 2220 gtcaaggtgg tggatgaatt ggtcaaggta atgggcagac ataagccaga aaatattgtg 2280 atcgagatgg cccgcgaaaa ccagaccaca cagaagggcc agaaaaatag tagagagcgg 2340 atgaagagga tcgaggaggg catcaaagag ctgggatctc agattctcaa agaacacccc 2400 gtagaaaaca cacagctgca gaacgaaaaa ttgtacttgt actatctgca gaacggcaga 2460 gacatgtacg tcgaccaaga acttgatatt aatagactgt ccgactatga cgtagaccat 2520 atcgtgcccc agtccttcct gaaggacgac tccattgata acaaagtctt gacaagaagc 2580 gacaagaaca ggggtaaaag tgataatgtg cctagcgagg aggtggtgaa aaaaatgaag 2640 aactactggc gacagctgct taatgcaaag ctcattacac aacggaagtt cgataatctg 2700 acgaaagcag agagaggtgg cttgtctgag ttggacaagg cagggtttat taagcggcag 2760 ctggtggaaa ctaggcagat cacaaagcac gtggcgcaga ttttggacag ccggatgaac 2820 acaaaatacg acgaaaatga taaactgata cgagaggtca aagttatcac gctgaaaagc 2880 aagctggtgt ccgattttcg gaaagacttc cagttctaca aagttcgcga gattaataac 2940 taccatcatg ctcacgatgc gtacctgaac gctgttgtcg ggaccgcctt gataaagaag 3000 tacccaaagc tggaatccga gttcgtatac ggggattaca aagtgtacga tgtgaggaaa 3060 atgatagcca agtccgagca ggagattgga aaggccacag ctaagtactt cttttattct 3120 aacatcatga atttttttaa gacggaaatt accctggcca acggagagat cagaaagcgg 3180 ccccttatag agacaaatgg tgaaacaggt gaaatcgtct gggataaggg cagggatttc 3240 gctactgtga ggaaggtgct gagtatgcca caggtaaata tcgtgaaaaa aaccgaagta 3300 cagaccggag gattttccaa ggaaagcatt ttgcctaaaa gaaactcaga caagctcatc 3360 gcccgcaaga aagattggga ccctaagaaa tacgggggat ttgactcacc caccgtagcc 3420 tattctgtgc tggtggtagc taaggtggaa aaaggaaagt ctaagaagct gaagtccgtg 3480 aaggaactct tgggaatcac tatcatggaa agatcatcct ttgaaaagaa ccctatcgat 3540 ttcctggagg ctaagggtta caaggaggtc aagaaagacc tcatcattaa actgccaaaa 3600 tactctctct tcgagctgga aaatggcagg aagagaatgt tggccagcgc cggagagctg 3660 caaaagggaa acgagcttgc tctgccctcc aaatatgtta attttctcta tctcgcttcc 3720 cactatgaaa agctgaaagg gtctcccgaa gataacgagc agaagcagct gttcgtcgaa 3780 cagcacaagc actatctgga tgaaataatc gaacaaataa gcgagttcag caaaagggtt 3840 atcctggcgg atgctaattt ggacaaagta ctgtctgctt ataacaagca ccgggataag 3900 cctattaggg aacaagccga gaatataatt cacctcttta cactcacgaa tctcggagcc 3960 cccgccgcct tcaaatactt tgatacgact atcgaccgga aacggtatac cagtaccaaa 4020 gaggtcctcg atgccaccct catccaccag tcaattactg gcctgtacga aacacggatc 4080 gacctctctc aactgggcgg cgactag 4107

If the above Cas9 sequences are fused with a peptide or polypeptide at the C-terminus (e.g., an inactive Cas9 fused with a transcription repressor at the C-terminus), it is understood that the stop codon will be removed.

VI. Functional Analysis of Candidate Molecules

Candidate Cas9 molecules, candidate gRNA molecules, candidate Cas9 molecule/gRNA molecule complexes, can be evaluated by art-known methods or as described herein. For example, exemplary methods for evaluating the endonuclease activity of Cas9 molecule are described, e.g., in Jinek el al., SCIENCE 2012; 337(6096):816-821.

VII. Template Nucleic Acids (For Introduction of Nucleic Acids)

The term “template nucleic acid” or “donor template” as used herein refers to a nucleic acid to be inserted at or near a target sequence that has been modified, e.g., cleaved, by a CRISPR system of the present invention. In an embodiment, nucleic acid sequence at or near the target sequence is modified to have some or all of the sequence of the template nucleic acid, typically at or near cleavage site(s). In an embodiment, the template nucleic acid is single stranded. In an alternate embodiment, the template nucleic acid is double stranded. In an embodiment, the template nucleic acid is DNA, e.g., double stranded DNA. In an alternate embodiment, the template nucleic acid is single stranded DNA.

In embodiments, the template nucleic acid comprises sequence encoding a globin protein, e.g., a beta globin, e.g., comprises a beta globin gene. In an embodiment, the beta globin encoded by the nucleic acid comprises one or more mutations, e.g., anti-sickling mutations. In an embodiment, the beta globin encoded by the nucleic acid comprises the mutation T87Q. In an embodiment, the beta globin encoded by the nucleic acid comprises the mutation G16D. In an embodiment, the beta globin encoded by the nucleic acid comprises the mutation E22A. In an embodiment, the beta globin gene comprises the mutations G16D, E22A and T87Q. In embodiments, the template nucleic acid further comprises one or more regulatory elements, e.g., a promoter (e.g., a human beta globin promoter), a 3′ enhancer, and/or at least a portion of a globin locus control region (e.g., one or more DNAseI hypersensitivity sites (e.g., HS2, HS3 and/or HS4 of the human globin locus)).

In other embodiments, the template nucleic acid comprises sequence encoding a gamma globin, e.g., comprises a gamma globin gene. In embodiments, the template nucleic acid comprises sequence encoding more than one copy of a gamma globin protein, e.g., comprises two or more, e.g., two, gamma globin gene sequences. In embodiments, the template nucleic acid further comprises one or more regulatory elements, e.g., a promotor and/or enhancer.

In an embodiment, the template nucleic acid alters the structure of the target position by participating in a homology directed repair event. In an embodiment, the template nucleic acid alters the sequence of the target position. In an embodiment, the template nucleic acid results in the incorporation of a modified, or non-naturally occurring base into the target nucleic acid.

Mutations in a gene or pathway described herein may be corrected using one of the approaches discussed herein. In an embodiment, a mutation in a gene or pathway described herein is corrected by homology directed repair (HDR) using a template nucleic acid. In an embodiment, a mutation in a gene or pathway described herein is corrected by homologous recombination (HR) using a template nucleic acid. In an embodiment, a mutation in a gene or pathway described herein is corrected by Non-Homologous End Joining (NHEJ) repair using a template nucleic acid. In other embodiments, nucleic acid encoding molecules of interest may be inserted at or near a site modified by a CRISPR system of the present invention. In embodiments, the template nucleic acid comprises regulatory elements, e.g., one or more promotors and/or enhancers, operably linked to the nucleic acid sequence encoding a molecule of interest, e.g., as described herein.

HDR or HR Repair and Template Nucleic Acids

As described herein, nuclease-induced homology directed repair (HDR) or homologous recombination (HR) can be used to alter a target sequence and correct (e.g., repair or edit) a mutation in the genome. While not wishing to be bound by theory, it is believed that alteration of the target sequence occurs by repair based on a donor template or template nucleic acid. For example, the donor template or the template nucleic acid provides for alteration of the target sequence. It is contemplated that a plasmid donor or linear double stranded template can be used as a template for homologous recombination. It is further contemplated that a single stranded donor template can be used as a template for alteration of the target sequence by alternate methods of homology directed repair (e.g., single strand annealing) between the target sequence and the donor template. Donor template-effected alteration of a target sequence may depend on cleavage by a Cas9 molecule. Cleavage by Cas9 can comprise a double strand break, one single strand break, or two single strand breaks.

In an embodiment, a mutation can be corrected by either a single double-strand break or two single strand breaks. In an embodiment, a mutation can be corrected by providing a template and a CRISPR/Cas9 system that creates (1) one double strand break, (2) two single strand breaks, (3) two double stranded breaks with a break occurring on each side of the target sequence, (4) one double stranded break and two single strand breaks with the double strand break and two single strand breaks occurring on each side of the target sequence, (5) four single stranded breaks with a pair of single stranded breaks occurring on each side of the target sequence, or (6) one single strand break.

Double Strand Break Mediated Correction

In an embodiment, double strand cleavage is effected by a Cas9 molecule having cleavage activity associated with an HNH-like domain and cleavage activity associated with a RuvC-like domain, e.g., an N-terminal RuvC-like domain, e.g., a wild type Cas9. Such embodiments require only a single gRNA.

Single Strand Break Mediated Correction

In other embodiments, two single strand breaks, or nicks, are effected by a Cas9 molecule having nickase activity, e.g., cleavage activity associated with an HNH-like domain or cleavage activity associated with an N-terminal RuvC-like domain Such embodiments require two gRNAs, one for placement of each single strand break. In an embodiment, the Cas9 molecule having nickase activity cleaves the strand to which the gRNA hybridizes, but not the strand that is complementary to the strand to which the gRNA hybridizes. In an embodiment, the Cas9 molecule having nickase activity does not cleave the strand to which the gRNA hybridizes, but rather cleaves the strand that is complementary to the strand to which the gRNA hybridizes.

In an embodiment, the nickase has HNH activity, e.g., a Cas9 molecule having the RuvC activity inactivated, e.g., a Cas9 molecule having a mutation at D10, e.g., the D10A mutation. D10A inactivates RuvC; therefore, the Cas9 nickase has (only) HN H activity and will cut on the strand to which the gRNA hybridizes (e.g., the complementary strand, which does not have the NGG PAM on it). In other embodiments, a Cas9 molecule having an H840, e.g., an H840A, mutation can be used as a nickase. H840A inactivates HNH; therefore, the Cas9 nickase has (only) RuvC activity and cuts on the non-complementary strand (e.g., the strand that has the NGG PAM and whose sequence is identical to the gRNA).

In an embodiment, in which a nickase and two gRNAs are used to position two single strand nicks, one nick is on the + strand and one nick is on the − strand of the target nucleic acid. The PAMs are outwardly facing. The gRNAs can be selected such that the gRNAs are separated by, from about 0-50, 0-100, or 0-200 nucleotides. In an embodiment, there is no overlap between the target sequence that is complementary to the targeting domains of the two gRNAs. In an embodiment, the gRNAs do not overlap and are separated by as much as 50, 100, or 200 nucleotides. In an embodiment, the use of two gRNAs can increase specificity, e.g., by decreasing off-target binding (Ran el cil., CELL 2013).

In an embodiment, a single nick can be used to induce HDR. It is contemplated herein that a single nick can be used to increase the ratio of HDR, HR or NHEJ at a given cleavage site.

Placement of the Double Strand Break or a Single Strand Break Relative to Target Position

The double strand break or single strand break in one of the strands should be sufficiently close to target position such that correction occurs. In an embodiment, the distance is not more than 50, 100, 200, 300, 350 or 400 nucleotides. While not wishing to be bound by theory, it is believed that the break should be sufficiently close to target position such that the break is within the region that is subject to exonuclease-mediated removal during end resection. If the distance between the target position and a break is too great, the mutation may not be included in the end resection and, therefore, may not be corrected, as donor sequence may only be used to correct sequence within the end resection region.

In an embodiment, in which a gRNA (unimolecular (or chimeric) or modular gRNA) and Cas9 nuclease induce a double strand break for the purpose of inducing HDR- or HR-mediated correction, the cleavage site is between 0-200 bp (e.g., 0 to 175, 0 to 150, 0 to 125, 0 to 100, 0 to 75, 0 to 50, 0 to 25, 25 to 200, 25 to 175, 25 to 150, 25 to 125, 25 to 100, 25 to 75, 25 to 50, 50 to 200, 50 to 175, 50 to 150, 50 to 125, 50 to 100, 50 to 75, 75 to 200, 75 to 175, 75 to 150, 75 to 125, 75 to 100 bp) away from the target position. In an embodiment, the cleavage site is between 0-100 bp (e.g., 0 to 75, 0 to 50, 0 to 25, 25 to 100, 25 to 75, 25 to 50, 50 to 100, 50 to 75 or 75 to 100 bp) away from the target position.

In an embodiment, in which two gRNAs (independently, unimolecular (or chimeric) or modular gRNA) complexing with Cas9 nickases induce two single strand breaks for the purpose of inducing HDR-mediated correction, the closer nick is between 0-200 bp (e.g., 0 to 175, 0 to 150, 0 to 125, 0 to 100, 0 to 75, 0 to 50, 0 to 25, 25 to 200, 25 to 175, 25 to 150, 25 to 125, 25 to 100, 25 to 75, 25 to 50, 50 to 200, 50 to 175, 50 to 150, 50 to 125, 50 to 100, 50 to 75, 75 to 200, 75 to 175, 75 to 150, 75 to 125, 75 to 100 bp) away from the target position and the two nicks will ideally be within 25-55 bp of each other (e.g., 25 to 50, 25 to 45, 25 to 40, 25 to 35, 25 to 30, 30 to 55, 30 to 50, 30 to 45, 30 to 40, 30 to 35, 35 to 55, 35 to 50, 35 to 45, 35 to 40, 40 to 55, 40 to 50, 40 to 45 bp) and no more than 100 bp away from each other (e.g., no more than 90, 80, 70, 60, 50, 40, 30, 20, 10 or 5 bp away from each other). In an embodiment, the cleavage site is between 0-100 bp (e.g., 0 to 75, 0 to 50, 0 to 25, 25 to 100, 25 to 75, 25 to 50, 50 to 100, 50 to 75 or 75 to 100 bp) away from the target position.

In one embodiment, two gRNAs, e.g., independently, unimolecular (or chimeric) or modular gRNA, are configured to position a double-strand break on both sides of a target position. In an alternate embodiment, three gRNAs, e.g., independently, unimolecular (or chimeric) or modular gRNA, are configured to position a double strand break (i.e., one gRNA complexes with a Cas9 nuclease) and two single strand breaks or paired single stranded breaks (i.e., two gRNAs complex with Cas9 nickases) on either side of the target position (e.g., the first gRNA is used to target upstream (i.e., 5′) of the target position and the second gRNA is used to target downstream (i.e., 3′) of the target position). In another embodiment, four gRNAs, e.g., independently, unimolecular (or chimeric) or modular gRNA, are configured to generate two pairs of single stranded breaks (i.e., two pairs of two gRNAs complex with Cas9 nickases) on either side of the target position (e.g., the first gRNA is used to target upstream (i.e., 5′) of the target position and the second gRNA is used to target downstream (i.e., 3′) of the target position). The double strand break(s) or the closer of the two single strand nicks in a pair will ideally be within 0-500 bp of the target position (e.g., no more than 450, 400, 350, 300, 250, 200, 150, 100, 50 or 25 bp from the target position). When nickases are used, the two nicks in a pair are within 25-55 bp of each other (e.g., between 25 to 50, 25 to 45, 25 to 40, 25 to 35, 25 to 30, 50 to 55, 45 to 55, 40 to 55, 35 to 55, 30 to 55, 30 to 50, 35. to 50, 40 to 50, 45 to 50, 35 to 45, or 40 to 45 bp) and no more than 100 bp away from each other (e.g., no more than 90, 80, 70, 60, 50, 40, 30, 20 or 10 bp).

In one embodiment, two gRNAs, e.g., independently, unimolecular (or chimeric) or modular gRNA, are configured to position a double-strand break on both sides of a target position. In an alternate embodiment, three gRNAs, e.g., independently, unimolecular (or chimeric) or modular gRNA, are configured to position a double strand break (i.e., one gRNA complexes with a Cas9 nuclease) and two single strand breaks or paired single stranded breaks (i.e., two gRNAs complex with Cas9 nickases) on two target sequences (e.g., the first gRNA is used to target an upstream (i.e., 5′) target sequence and the second gRNA is used to target a downstream (i.e., 3′) target sequence of an insertion site. In another embodiment, four gRNAs, e.g., independently, unimolecular (or chimeric) or modular gRNA, are configured to generate two pairs of single stranded breaks (i.e., two pairs of two gRNAs complex with Cas9 nickases) on either side of an insertion site (e.g., the first gRNA is used to target an upstream (i.e., 5′) target sequence described herein, and the second gRNA is used to target a downstream (i.e., 3′) target sequence described herein). The double strand break(s) or the closer of the two single strand nicks in a pair will ideally be within 0-500 bp of the target position (e.g., no more than 450, 400, 350, 300, 250, 200, 150, 100, 50 or 25 bp from the target position). When nickases are used, the two nicks in a pair are within 25-55 bp of each other (e.g., between 25 to 50, 25 to 45, 25 to 40, 25 to 35, 25 to 30, 50 to 55, 45 to 55, 40 to 55, 35 to 55, 30 to 55, 30 to 50, 35 to 50, 40 to 50, 45 to 50, 35 to 45, or 40 to 45 bp) and no more than 100 bp away from each other (e.g., no more than 90, 80, 70, 60, 50, 40, 30, 20 or 10 bp).

Length of the Homology Arms

The homology arm should extend at least as far as the region in which end resection may occur, e.g., in order to allow the resected single stranded overhang to find a complementary region within the donor template. The overall length could be limited by parameters such as plasmid size or viral packaging limits. In an embodiment, a homology arm does not extend into repeated elements, e.g., ALU repeats, LINE repeats. A template may have two homology arms of the same or different lengths.

Exemplary Homology Arm Lengths Include at Least 25, 50, 100, 250, 500, 750 or 1000 Nucleotides.

Target position, as used herein, refers to a site on a target nucleic acid (e.g., the chromosome) that is modified by a Cas9 molecule-dependent process. For example, the target position can be a modified Cas9 molecule cleavage of the target nucleic acid and template nucleic acid directed modification, e.g., correction, of the target position. In an embodiment, a target position can be a site between two nucleotides, e.g., adjacent nucleotides, on the target nucleic acid into which one or more nucleotides is added. The target position may comprise one or more nucleotides that are altered, e.g., corrected, by a template nucleic acid. In an embodiment, the target position is within a target sequence (e.g., the sequence to which the gRN A binds) In an embodiment, a target position is upstream or downstream of a target sequence (e.g., the sequence to which the gRNA binds).

Typically, the template sequence undergoes a breakage mediated or catalyzed recombination with the target sequence. In an embodiment, the template nucleic acid includes sequence that corresponds to a site on the target sequence that is cleaved by a Cas9 mediated cleavage event. In an embodiment, the template nucleic acid includes sequence that corresponds to both, a first site on the target sequence that is cleaved in a first Cas9 mediated event, and a second site on the target sequence that is cleaved in a second Cas9 mediated event.

In an embodiment, the template nucleic acid can include sequence which results in an alteration in the coding sequence of a translated sequence, e.g., one which results in the substitution of one amino acid for another in a protein product, e.g., transforming a mutant allele into a wild type allele, transforming a wild type allele into a mutant allele, and/or introducing a stop codon, insertion of an amino acid residue, deletion of an amino acid residue, or a nonsense mutation.

In other embodiments, the template nucleic acid can include sequence which results in an alteration in a non-coding sequence, e.g., an alteration in an exon or in a 5′ or 3′ non-translated or non-transcribed region. Such alterations include an alteration in a control element, e.g., a promoter, enhancer, and an alteration in a cis-acting or trans-acting control element.

The template nucleic acid can include sequence which, when integrated, results in:

decreasing the activity of a positive control element; increasing the activity of a positive control element; decreasing the activity of a negative control element; increasing the activity of a negative control element; decreasing the expression of a gene; increasing the expression of a gene; increasing resistance to a disorder or disease; increasing resistance to viral entry; correcting a mutation or altering an unwanted amino acid residue; conferring, increasing, abolishing or decreasing a biological property of a gene product, e.g., increasing the enzymatic activity of an enzyme, or increasing the ability of a gene product to interact with another molecule.

The template nucleic acid can include sequence which results in:

a change in sequence of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 or more nucleotides of the target sequence.

In an embodiment, the template nucleic acid is 20+/−10, 30+/−10, 40+/−10, 50+/−10, 60+/−10, 70+/−10, 80+/−10, 90+/−10, 100+/−10, 110+/−10, 120+/−10, 130+/−10, 140+/−10, 150+/−10, 160+/−10, 170+/−10, 180+/−10, 190+/−10, 200+/−10, 210+/−10, 220+/−10, 200-300, 300-400, 400-500, 500-600, 600-700, 700-800, 800-900, 900-1000, 1000-2000, 2000-3000 or more than 3000 nucleotides in length.

A template nucleic acid comprises the following components:

[5′ homology arm]-[insertion sequence]-[3′ homology arm].

The homology arms provide for recombination into the chromosome, which can replace the undesired element, e.g., a mutation or signature, with the replacement sequence. In an embodiment, the homology arms flank the most distal cleavage sites.

In an embodiment, the 3′ end of the 5′ homology arm is the position next to the 5′ end of the replacement sequence. In an embodiment, the 5′ homology arm can extend at least 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 120, 150, 180, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1500, or 2000 nucleotides 5′ from the 5′ end of the replacement sequence.

In an embodiment, the 5′ end of the 3′ homology arm is the position next to the 3′ end of the replacement sequence. In an embodiment, the 3′ homology arm can extend at least 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 120, 150, 180, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1500, or 2000 nucleotides 3′ from the 3′ end of the replacement sequence.

It is contemplated herein that one or both homology arms may be shortened to avoid including certain sequence repeat elements, e.g., Alu repeats, LINE elements. For example, a 5′ homology arm may be shortened to avoid a sequence repeat element. In other embodiments, a 3′ homology arm may be shortened to avoid a sequence repeat element. In some embodiments, both the 5′ and the 3′ homology arms may be shortened to avoid including certain sequence repeat elements.

It is contemplated herein that template nucleic acids for correcting a mutation may designed for use as a single-stranded oligonucleotide (ssODN). When using a ssODN, 5′ and 3′ homology arms may range up to about 200 base pairs (bp) in length, e.g., at least 25, 50, 75, 100, 125, 150, 175, or 200 bp in length. Longer homology arms are also contemplated for ssODNs as improvements in oligonucleotide synthesis continue to be made.

NHEJ Approaches for Gene Targeting

As described herein, nuclease-induced non-homologous end-joining (NHEJ) can be used to target gene-specific knockouts. Nuclease-induced NHEJ can also be used to remove (e.g., delete) sequence in a gene of interest.

While not wishing to be bound by theory, it is believed that, in an embodiment, the genomic alterations associated with the methods described herein rely on nuclease-induced NHEJ and the error-prone nature of the NHEJ repair pathway. NHEJ repairs a double-strand break in the DNA by joining together the two ends; however, generally, the original sequence is restored only if two compatible ends, exactly as they were formed by the double-strand break, are perfectly ligated. The DNA ends of the double-strand break are frequently the subject of enzymatic processing, resulting in the addition or removal of nucleotides, at one or both strands, prior to rejoining of the ends. This results in the presence of insertion and/or deletion (indel) mutations in the DNA sequence at the site of the NHEJ repair. Two-thirds of these mutations may alter the reading frame and, therefore, produce a non-functional protein. Additionally, mutations that maintain the reading frame, but which insert or delete a significant amount of sequence, can destroy functionality of the protein. This is locus dependent as mutations in critical functional domains are likely less tolerable than mutations in non-critical regions of the protein.

The indel mutations generated by NHEJ are unpredictable in nature; however, at a given break site certain indel sequences are favored and are over represented in the population. The lengths of deletions can vary widely; most commonly in the 1-50 bp range, but they can easily reach greater than 100-200 bp. Insertions tend to be shorter and often include short duplications of the sequence immediately surrounding the break site. However, it is possible to obtain large insertions, and in these cases, the inserted sequence has often been traced to other regions of the genome or to plasmid DNA present in the cells.

Because NHEJ is a mutagenic process, it can also be used to delete small sequence motifs as long as the generation of a specific final sequence is not required. If a double-strand break is targeted near to a short target sequence, the deletion mutations caused by the NHEJ repair often span, and therefore remove, the unwanted nucleotides. For the deletion of larger DNA segments, introducing two double-strand breaks, one on each side of the sequence, can result in NHEJ between the ends with removal of the entire intervening sequence. Both of these approaches can be used to delete specific DNA sequences; however, the error-prone nature of NHEJ may still produce indel mutations at the site of repair.

Both double strand cleaving Cas9 molecules and single strand, or nickase, Cas9 molecules can be used in the methods and compositions described herein to generate NHEJ-mediated indels. NHEJ-mediated indels targeted to the gene, e.g., a coding region, e.g., an early coding region of a gene of interest can be used to knockout (i.e., eliminate expression of) a gene of interest. For example, early coding region of a gene of interest includes sequence immediately following a transcription start site, within a first exon of the coding sequence, or within 500 bp of the transcription start site (e.g., less than 500, 450, 400, 350, 300, 250, 200, 150, 100 or 50 bp).

Placement of Double Strand or Single Strand Breaks Relative to the Target Position

In an embodiment, in which a gRNA and Cas9 nuclease generate a double strand break for the purpose of inducing NHEJ-mediated indels, a gRNA, e.g., a unimolecular (or chimeric) or modular gRNA molecule, is configured to position one double-strand break in close proximity to a nucleotide of the target position. In an embodiment, the cleavage site is between 0-500 bp away from the target position (e.g., less than 500, 400, 300, 200, 100, 50, 40, 30, 25, 20, 15, 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1 bp from the target position).

In an embodiment, in which two gRNAs complexing with Cas9 nickases induce two single strand breaks for the purpose of inducing NHEJ-mediated indels, two gRNAs, e.g., independently, unimolecular (or chimeric) or modular gRNA, are configured to position two single-strand breaks to provide for NHEJ repair a nucleotide of the target position. In an embodiment, the gRNAs are configured to position cuts at the same position, or within a few nucleotides of one another, on different strands, essentially mimicking a double strand break. In an embodiment, the closer nick is between 0-30 bp away from the target position (e.g., less than 30, 25, 20, 1, 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1 bp from the target position), and the two nicks are within 25-55 bp of each other (e.g., between 25 to 50, 25 to 45, 25 to 40, 25 to 35, 25 to 30, 50 to 55, 45 to 55, 40 to 55, 35 to 55, 30 to 55, 30 to 50, 35 to 50, 40 to 50, 45 to 50, 35 to 45, or 40 to 45 bp) and no more than 100 bp away from each other (e.g., no more than 90, 80, 70, 60, 50, 40, 30, 20 or 10 bp). In an embodiment, the gRNAs are configured to place a single strand break on either side of a nucleotide of the target position.

Both double strand cleaving Cas9 molecules and single strand, or nickase, Cas9 molecules can be used in the methods and compositions described herein to generate breaks both sides of a target position. Double strand or paired single strand breaks may be generated on both sides of a target position to remove the nucleic acid sequence between the two cuts (e.g., the region between the two breaks is deleted). In one embodiment, two gRNAs, e.g., independently, unimolecular (or chimeric) or modular gRNA, are configured to position a double-strand break on both sides of a target position (e.g., the first gRNA is used to target upstream (i.e., 5′) of the mutation in a gene or pathway described herein, and the second gRNA is used to target downstream (i.e., 3′) of the mutation in a gene or pathway described herein). In an alternate embodiment, three gRNAs, e.g., independently, unimolecular (or chimeric) or modular gRNA, are configured to position a double strand break (i.e., one gRNA complexes with a Cas9 nuclease) and two single strand breaks or paired single stranded breaks (i.e., two gRNAs complex with Cas9 nickases) on either side of a target position (e.g., the fu st gRNA is used to target upstream (i.e., 5′) of the mutation in a gene or pathway described herein, and the second gRNA is used to target downstream (i.e., 3′) of the mutation in a gene or pathway described herein). In another embodiment, four gRNAs, e.g., independently, unimolecular (or chimeric) or modular gRNA, are configured to generate two pairs of single stranded breaks (i.e., two pairs of two gRNAs complex with Cas9 nickases) on either side of the target position (e.g., the first gRNA is used to target upstream (i.e., 5′) of the mutation in a gene or pathway described herein, and the second gRNA is used to target downstream (i.e., 3′) of the mutation in a gene or pathway described herein). The double strand break(s) or the closer of the two single strand nicks in a pair will ideally be within 0-500 bp of the target position (e.g., no more than 450, 400, 350, 300, 250, 200, 150, 100, 50 or 25 bp from the target position). When nickases are used, the two nicks in a pair are within 25-55 bp of each other (e.g., between 25 to 50, 25 to 45, 25 to 40, 25 to 35, 25 to 30, 50 to 55, 45 to 55, 40 to 55, 35 to 55, 30 to 55, 30 to 50, 35 to 50, 40 to 50, 45 to 50, 35 to 45, or 40 to 45 bp) and no more than 100 bp away from each other (e.g., no more than 90, 80, 70, 60, 50, 40, 30, 20 or 10 bp).

In other embodiments, the insertion of template nucleic acid may be mediated by microhomology end joining (MMEJ). See, e.g., Saksuma et al., “MMEJ-assisted gene knock-in using TALENs and CRISPR-Cas9 with the PITCh systems.” Nature Protocols 11, 118-133 (2016) doi:10.1038/nprot.2015.140 Published online 17 Dec. 2015, the contents of which are incorporated by reference in their entirety.

VIII. Systems Comprising More Than One gRNA Molecule

While not intending to be bound by theory, it has been surprisingly shown herein that the targeting of two target sequences (e.g., by two gRNA molecule/Cas9 molecule complexes which each induce a single- or double-strand break at or near their respective target sequences) located in close proximity on a continuous nucleic acid induces excision (e.g., deletion) of the nucleic acid sequence (or at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% of the nucleic acid sequence) located between the two target sequences. In some aspects, the present disclosure provides for the use of two or more gRNA molecules that comprise targeting domains targeting target sequences in close proximity on a continuous nucleic acid, e.g., a chromosome, e.g., a gene or gene locus, including its introns, exons and regulatory elements. The use may be, for example, by introduction of the two or more gRNA molecules, together with one or more Cas9 molecules (or nucleic acid encoding the two or more gRNA molecules and/or the one or more Cas9 molecules) into a cell.

In some aspects, the target sequences of the two or more gRNA molecules are located at least 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000, 10,000, 11,000, 12,000, 13,000, 14,000, or 15,000 nucleotides apart on a continuous nucleic acid, but not more than 25,000 nucleotides apart on a continuous nucleic acid. In an embodiment, the target sequences are located about 4000 nucleotides apart. In an embodiment, the target sequences are located about 6000 nucleotides apart.

In some aspects, the plurality of gRNA molecules each target sequences within the same gene or gene locus. In another aspect, the plurality of gRNA molecules each target sequences within 2 or more different genes.

In some aspects, the invention provides compositions and cells comprising a plurality, for example, 2 or more, for example, 2, gRNA molecules of the invention, wherein the plurality of gRNA molecules target sequences less than 15,000, less than 14,000, less than 13,000, less than 12,000, less than 11,000, less than 10,000, less than 9,000, less than 8,000, less than 7,000, less than 6,000, less than 5,000, less than 4,000, less than 3,000, less than 2,000, less than 1,000, less than 900, less than 800, less than 700, less than 600, less than 500, less than 400, less than 300, less than 200, less than 100, less than 90, less than 80, less than 70, less than 60, less than 50, less than 40, or less than 30 nucleotides apart. In an embodiment, the target sequences are on the same strand of duplex nucleic acid. In an embodiment, the target sequences are on different strands of duplex nucleic acid.

In one embodiment, the invention provides a method for excising (e.g., deleting) nucleic acid disposed between two gRNA binding sites disposed less than 25,000, less than 20,000, less than 15,000, less than 14,000, less than 13,000, less than 12,000, less than 11,000, less than 10,000, less than 9,000, less than 8,000, less than 7,000, less than 6,000, less than 5,000, less than 4,000, less than 3,000, less than 2,000, less than 1,000, less than 900, less than 800, less than 700, less than 600, less than 500, less than 400, less than 300, less than 200, less than 100, less than 90, less than 80, less than 70, less than 60, less than 50, less than 40, or less than 30 nucleotides apart on the same or different strands of duplex nucleic acid. In an embodiment, the method provides for deletion of more than 50%, more than 60%, more than 70%, more than 80%, more than 85%, more than 86%, more than 87%, more than 88%, more than 89%, more than 90%, more than 91%, more than 92%, more than 93%, more than 94%, more than 95%, more than 96%, more than 97%, more than 98%, more than 99%, or 100% of the nucleotides disposed between the PAM sites associated with each gRNA binding site. In embodiments, the deletion further comprises of one or more nucleotides within one or more of the PAM sites associated with each gRNA binding site. In embodiments, the deletion also comprises one or more nucleotides outside of the region between the PAM sites associated with each gRNA binding site.

In one aspect, the two or more gRNA molecules comprise targeting domains targeting target sequences flanking a gene regulatory element, e.g., a promotor binding site, an enhancer region, or a repressor region, such that excision of the intervening sequence (or a portion of the intervening sequence) causes up- or down-regulation of a gene of interest.

In an embodiment, the two or more gRNA molecules include targeting domains comprising, e.g., consisting of, a targeting domain sequence of Table 1 or Table 5. In aspects, the two or more gRNA molecules comprise targeting domains that are complementary with sequences in the same gene. In aspects, the two or more gRNA molecules comprise targeting domains that are complementary with sequences of different genes. In an embodiment, the two or more gRNA molecules include targeting domains comprising, e.g., consisting of, a targeting domain sequence of Table 6. In an embodiment, the two or more gRNA molecules include targeting domains comprising, e.g., consisting of, a targeting domain sequence of Table 2, Table 7, Table 8 and/or Table 9. In aspects, the two or more gRNA molecules comprise targeting domains that are complementary with sequences in the same gene. In aspects, the two or more gRNA molecules comprise targeting domains that are complementary with sequences of different genes. In an embodiment, the two or more gRNA molecules are selected from the gRNA molecules of Table 7, Table 8 and/or Table 9. In an embodiment, the first and second gRNA molecules comprise targeting domains comprising, e.g., consisting of, targeting domain sequences selected from Tables 1-9, and are selected from different tables, e.g., and comprise targeting domains that are complementary with sequences of different genes.

In one aspect, the two or more gRNA molecules comprise targeting domains targeting target sequences flanking a gene regulatory element, e.g., a promotor binding site, an enhancer region, or a repressor region, such that excision of the intervening sequence (or a portion of the intervening sequence) causes up- or down-regulation of a gene of interest. By way of example, the two or more gRNA molecules comprise targeting domains targeting target sequences flanking a GATA1 binding site (or portion thereof) or TAL1 binding site (or portion thereof) of the erythroid enhancer region of the BCL11a gene (e.g., within the +55, +58 or +62 region). In other embodiments, the gRNA molecule or molecules do not result in a disruption of the GATA1 binding site or TAL1 binding site within the BCL11a Enhancer.

In an embodiment, the two or more gRNA molecules comprise targeting domains that comprise, e.g., consist of, targeting domains selected from Table 1. In an embodiment, the two or more gRNA molecules comprise targeting domains that comprise, e.g., consist of, targeting domains selected from Table 2. In an embodiment, the two or more gRNA molecules comprise targeting domains that comprise, e.g., consist of, targeting domains selected from Table 3. In an embodiment, the two or more gRNA molecules comprise targeting domains that comprise, e.g., consist of, targeting domains selected from Table 4. In an embodiment, the two or more gRNA molecules comprise targeting domains that comprise, e.g., consist of, targeting domains selected from Table 5. In an embodiment, the two or more gRNA molecules comprise targeting domains that comprise, e.g., consist of, targeting domains selected from Table 6. In an embodiment, the two or more gRNA molecules comprise targeting domains that comprise, e.g., consist of, targeting domains selected from Table 7. In an embodiment, the two or more gRNA molecules comprise targeting domains that comprise, e.g., consist of, targeting domains selected from Table 8. In an embodiment, the two or more gRNA molecules comprise targeting domains that comprise, e.g., consist of, targeting domains selected from Table 9.

In aspects, the two or more gRNA molecules comprise targeting domains comprising, e.g., consisting of the targeting domain sequence pairs listed in section II, above.

Without being bound by theory, it is believed that increasing the expression of fetal hemoglobin (e.g., gamma globin) while simultaneously reducing or eliminating expression of beta globin (e.g., beta globin comprising a sickling mutation), will result in increased efficacy in treating a hemoglobinopathy, e.g., sickle cell disease. Thus, in one aspect, the two or more gRNA molecules comprise a first gRNA molecule that causes an increase in gamma globin expression and a second gRNA molecule that reduces or eliminates expression of beta globin, e.g., beta globin carrying a sickle cell mutation. In embodiments, the two or more gRNA molecules comprise a first gRNA molecule that targets a sequence within a BCL11a enhancer region, e.g., as described herein, e.g., a gRNA molecule comprising a targeting domain comprising, e.g., consisting of, a targeting domain of Table 7, Table 8 or Table 9, and a second gRNA molecule that targets a sequence of a sickle globin gene (e.g., a beta globin gene comprising a sickling mutation).

IX. Properties of the gRNA

It has further been surprisingly shown herein that gRNA molecules and CRISPR systems comprising said gRNA molecules produce similar or identical indel patterns across multiple experiments using the same cell type, method of delivery and crRNA/tracr components. Without being bound by theory, it is believed that some indel patterns may be more advantageous than others. For example, indels which predominantly include insertions and/or deletions which result in a “frameshift mutation” (e.g., 1- or 2-base pair insertion or deletions, or any insertion or deletion where n/3 is not a whole number (where n=the number of nucleotides in the insertion or deletion)) may be beneficial in reducing or eliminating expression of a functional protein. Likewise, indels which predominantly include “large deletions” (deletions of more than 10, 11, 12, 13, 14, 15, 20, 25, or 30 nucleotides) may also be beneficial in, for example, removing critical regulatory sequences such as promoter binding sites, which may similarly have an improved effect on expression of functional protein. While the indel patterns induced by a given gRNA/CRISPR system have surprisingly been found to be consistently reproduced across cell types, as described herein, not any single indel structure will inevitably be produced in a given cell upon introduction of a gRNA/CRISPR system.

The invention thus provides for gRNA molecules which create a beneficial indel pattern or structure, for example, which have indel patterns or structures predominantly composed of frameshift mutation(s) and/or large deletions. Such gRNA molecules may be selected by assessing the indel pattern or structure created by a candidate gRNA molecule in a test cell (for example, a HEK293 cell) or in the cell of interest, e.g., a HSPC cell by NGS, as described herein. As shown in the Examples, gRNA molecules have been discovered, which, when introduced into the desired cell population, result in a population of cells comprising a significant fraction of the cells having a frameshift mutation in the targeted gene. In some cases, the rate of frameshift mutation is as high as 75%, 80%, 85%, 90% or more. The invention thus provides for populations of cells which comprise at least about 40% of cells (e.g., at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or at least about 99%) having a frameshift mutation, e.g., as described herein, at or near the target site of a gRNA moleucle described herein. The invention also provides for populations of cells which comprise at least about 50% of cells (e.g., at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or at least about 99%) having a frameshift mutation, e.g., as described herein, at or near the target site of a gRNA moleucle described herein.

The invention thus provides methods of selecting gRNA molecules for use in the therapeutic methods of the invention comprising: 1) providing a plurality of gRNA molecules to a target of interest, 2) assessing the indel pattern or structure created by use of said gRNA molecules, 3) selecting a gRNA molecule that forms an indel pattern or structure composed predominantly of frameshift mutations, large deletions or a combination thereof, and 4) using said selected gRNA in a methods of the invention.

The invention further provides methods of altering cells, and altered cells, wherein a particular indel pattern is consistently produced with a given gRNA/CRISPR system in that cell type. The indel patterns, including the top 5 most frequently occurring indels observed with the gRNA/CRISPR systems described herein are disclosed, for example, in the Examples. As shown in the examples, populations of cells are generated, wherein a significant fraction of the cells comprises one of the top 5 indels (for example, populations of cells wherein one of the top 5 indels is present in more than 30%, more than 40%, more than 50%, more than 60% or more of the cells of the population. Thus, the invention provides cells, e.g., HSPCs (as described herein), which comprise an indel of any one of the top 5 indels observed with a given gRNA/CRISPR system. Further, the invention provides populations of cells, e.g., HSPCs (as described herein), which when assessed by, for example, NGS, comprise a high percentage of cells comprising one of the top 5 indels described herein for a given gRNA/CRISPR system. When used in connection with indel pattern analysis, a “high percentage” refers to at least about 50% (e.g., at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or at least about 99%) of the cells of the population comprising one of the top 5 indels described herein for a given gRNA/CRISPR system. In other embodiments, the population of cells comprises at least about 25% (e.g., from about 25% to about 60%, e.g., from about 25% to about 50%, e.g., from about 25% to about 40%, e.g., from about 25% to about 35%) of cells which have one of the top 5 indels described herein for a given gRNA/CRISPR system. In embodiments, the top indels, e.g., top 5 indels for a given gRNA/CRISPR system which targets a +58 region of the BCL11a enhancer are provided in Table 15, FIG. 25, and Table 37. In embodiments, the top indels, e.g., top 5 indels for a given gRNA/CRISPR system which targets a HPFH region are provided in Table 26, Table 27 and Table 37.

It has also been discovered that certain gRNA molecules do not create indels at off-target sequences within the genome of the target cell type, or produce indels at off target sites at very low frequencies (e.g., <5% of cells within a population) relative to the frequency of indel creation at the target site. Thus, the invention provides for gRNA molecules and CRISPR systems which do not exhibit off-target indel formation in the target cell type, or which produce a frequency of off-target indel formation of <5%. In embodiments, the invention provides gRNA molecules and CRISPR systems which do not exhibit any off target indel formation in the target cell type. Thus, the invention further provides a cell, e.g., a population of cells, e.g., HSPCs, e.g., as described herein, which comprise an indel at or near a target site of a gRNA molecule described herein (e.g., a frameshift indel, or any one of the top 5 indels produced by a given gRNA/CRISPR system, e.g., as described herein), but does not comprise an indel at any off-target site of the gRNA molecule. In other embodiments, the invention further provides a a population of cells, e.g., HSPCs, e.g., as described herein, which comprises >50% of cells which have an indel at or near a target site of a gRNA molecule described herein (e.g., a frameshift indel, or any one of the top 5 indels produced by a given gRNA/CRISPR system, e.g., as described herein), but which comprises less than 5%, e.g., less than 4%, less than 3%, less than 2% or less than 1%, of cells comprising an indel at any off-target site of the gRNA molecule.

In embodiments, the indel produced by a CRISPR system described herein (e.g., a CRISPR system comprising a gRNA molecule described herein), does not comprise a nucleotide of a GATA-1 binding site and/or does not comprise a nucleotide of a TAL-1 binding site (e.g., does not comprise a nucleotide of a GATA-1 binding site and/or TAL-1 binding site described in FIG. 25).

X. Delivery/Constructs

The components, e.g., a Cas9 molecule or gRNA molecule, or both, can be delivered, formulated, or administered in a variety of forms. As a non-limiting example, the gRNA molecule and Cas9 molecule can be formulated (in one or more compositions), directly delivered or administered to a cell in which a genome editing event is desired. Alternatively, nucleic acid encoding one or more components, e.g., a Cas9 molecule or gRNA molecule, or both, can be formulated (in one or more compositions), delivered or administered. In one aspect, the gRNA molecule is provided as DNA encoding the gRNA molecule and the Cas9 molecule is provided as DNA encoding the Cas9 molecule. In one embodiment, the gRNA molecule and Cas9 molecule are encoded on separate nucleic acid molecules. In one embodiment, the gRNA molecule and Cas9 molecule are encoded on the same nucleic acid molecule. In one aspect, the gRNA molecule is provided as RNA and the Cas9 molecule is provided as DNA encoding the Cas9 molecule. In one embodiment, the gRNA molecule is provided with one or more modifications, e.g., as described herein. In one aspect, the gRNA molecule is provided as RNA and the Cas9 molecule is provided as mRNA encoding the Cas9 molecule. In one aspect, the gRNA molecule is provided as RNA and the Cas9 molecule is provided as a protein. In one embodiment, the gRNA and Cas9 molecule are provided as a ribonuclear protein complex (RNP). In one aspect, the gRNA molecule is provided as DNA encoding the gRNA molecule and the Cas9 molecule is provided as a protein.

Delivery, e.g., delivery of the RNP, (e.g., to HSPC cells as described herein) may be accomplished by, for example, electroporation (e.g., as known in the art) or other method that renders the cell membrane permeable to nucleic acid and/or polypeptide molecules. In embodiments, the CRISPR system, e.g., the RNP as described herein, is delivered by electroporation using a 4D-Nucleofector (Lonza), for example, using program CM-137 on the 4D-Nucleofector (Lonza). In embodiments, the CRISPR system, e.g., the RNP as described herein, is delivered by electroporation using a voltage from about 800 volts to about 2000 volts, e.g., from about 1000 volts to about 1800 volts, e.g., from about 1200 volts to about 1800 volts, e.g., from about 1400 volts to about 1800 volts, e.g., from about 1600 volts to about 1800 volts, e.g., about 1700 volts, e.g., at a voltage of 1700 volts. In embodiments, the pulse width/length is from about 10 ms to about 50 ms, e.g., from about 10 ms to about 40 ms, e.g., from about 10 ms to about 30 ms, e.g., from about 15 ms to about 25 ms, e.g., about 20 ms, e.g., 20 ms. In embodiments, 1, 2, 3, 4, 5, or more, e.g., 2, e.g., 1 pulses are used. In an embodiment, the CRISPR system, e.g., the RNP as described herein, is delivered by electroporation using a voltage of about 1700 volts (e.g., 1700 volts), a pulse width of about 20 ms (e.g., 20 ms), using a single (1) pulse. In embodiments, electroporation is accomplished using a Neon electroporator. Additional techniques for rendering the membrane permeable are known in the art and include, for example, cell squeezing (e.g., as described in WO2015/023982 and WO2013/059343, the contents of which are hereby incorporated by reference in their entirety), nanoneedles (e.g., as described in Chiappini et al., Nat. Mat., 14; 532-39, or US2014/0295558, the contents of which are hereby incorporated by reference in their entirety) and nanostraws (e.g., as described in Xie, ACS Nano, 7(5); 4351-58, the contents of which are hereby incorporated by reference in their entirety).

When a component is delivered encoded in DNA the DNA will typically include a control region, e.g., comprising a promoter, to effect expression. Useful promoters for Cas9 molecule sequences include CMV, EF-1alpha, MSCV, PGK, CAG control promoters. Useful promoters for gRNAs include H1, EF-1a and U6 promoters. Promoters with similar or dissimilar strengths can be selected to tune the expression of components. Sequences encoding a Cas9 molecule can comprise a nuclear localization signal (NLS), e.g., an SV40 NLS. In an embodiment, a promoter for a Cas9 molecule or a gRNA molecule can be, independently, inducible, tissue specific, or cell specific.

DNA-Based Delivery of a Cas9 Molecule and or a gRNA Molecule

DNA encoding Cas9 molecules and/or gRNA molecules, can be administered to subjects or delivered into cells by art-known methods or as described herein. For example, Cas9-encoding and/or gRNA-encoding DNA can be delivered, e.g., by vectors (e.g., viral or non-viral vectors), non-vector based methods (e.g., using naked DNA or DNA complexes), or a combination thereof.

In some embodiments, the Cas9- and/or gRNA-encoding DNA is delivered by a vector (e.g., viral vector/virus, plasmid, minicircle or nanoplasmid).

A vector can comprise a sequence that encodes a Cas9 molecule and/or a gRNA molecule. A vector can also comprise a sequence encoding a signal peptide (e.g., for nuclear localization, nucleolar localization, mitochondrial localization), fused, e.g., to a Cas9 molecule sequence. For example, a vector can comprise one or more nuclear localization sequence (e.g., from SV40) fused to the sequence encoding the Cas9 molecule.

One or more regulatory/control elements, e.g., a promoter, an enhancer, an intron, a polyadenylation signal, a Kozak consensus sequence, internal ribosome entry sites (IRES), a 2A sequence, and a splice acceptor or donor can be included in the vectors. In some embodiments, the promoter is recognized by RNA polymerase II (e.g., a CMV promoter). In other embodiments, the promoter is recognized by RNA polymerase III (e.g., a U6 promoter). In some embodiments, the promoter is a regulated promoter (e.g., inducible promoter). In other embodiments, the promoter is a constitutive promoter. In some embodiments, the promoter is a tissue specific promoter. In some embodiments, the promoter is a viral promoter. In other embodiments, the promoter is a non-viral promoter.

In some embodiments, the vector or delivery vehicle is a minicircle. In some embodiments, the vector or delivery vehicle is a nanoplasmid.

In some embodiments, the vector or delivery vehicle is a viral vector (e.g., for generation of recombinant viruses). In some embodiments, the virus is a DNA virus (e.g., dsDNA or ssDNA virus). In other embodiments, the virus is an RNA virus (e.g., an ssRNA virus).

Exemplary viral vectors/viruses include, e.g., retroviruses, lentiviruses, adenovirus, adeno-associated virus (AAV), vaccinia viruses, poxviruses, and herpes simplex viruses. Viral vector technology is well known in the art and is described, for example, in Sambrook et al., 2012, MOLECULAR CLONING: A LABORATORY MANUAL, volumes 1-4, Cold Spring Harbor Press, NY), and in other virology and molecular biology manuals.

In some embodiments, the virus infects dividing cells. In other embodiments, the virus infects non-dividing cells. In some embodiments, the virus infects both dividing and non-dividing cells. In some embodiments, the virus can integrate into the host genome. In some embodiments, the virus is engineered to have reduced immunity, e.g., in human. In some embodiments, the virus is replication-competent. In other embodiments, the virus is replication-defective, e.g., having one or more coding regions for the genes necessary for additional rounds of virion replication and/or packaging replaced with other genes or deleted. In some embodiments, the virus causes transient expression of the Cas9 molecule and/or the gRNA molecule. In other embodiments, the virus causes long-lasting, e.g., at least 1 week, 2 weeks, 1 month, 2 months, 3 months, 6 months, 9 months, 1 year, 2 years, or permanent expression, of the Cas9 molecule and/or the gRNA molecule. The packaging capacity of the viruses may vary, e.g., from at least about 4 kb to at least about 30 kb, e.g., at least about 5 kb, 10 kb, 15 kb, 20 kb, 25 kb, 30 kb, 35 kb, 40 kb, 45 kb, or 50 kb.

In some embodiments, the Cas9- and/or gRNA-encoding DNA is delivered by a recombinant retrovirus. In some embodiments, the retrovirus (e.g., Moloney murine leukemia virus) comprises a reverse transcriptase, e.g., that allows integration into the host genome. In some embodiments, the retrovirus is replication-competent. In other embodiments, the retrovirus is replication-defective, e.g., having one of more coding regions for the genes necessary for additional rounds of virion replication and packaging replaced with other genes, or deleted.

In some embodiments, the Cas9- and/or gRNA-encoding DNA is delivered by a recombinant lentivirus. For example, the lentivirus is replication-defective, e.g., does not comprise one or more genes required for viral replication.

In some embodiments, the Cas9- and/or gRNA-encoding DNA is delivered by a recombinant adenovirus. In some embodiments, the adenovirus is engineered to have reduced immunity in human.

In some embodiments, the Cas9- and/or gRNA-encoding DNA is delivered by a recombinant AAV. In some embodiments, the AAV can incorporate its genome into that of a host cell, e.g., a target cell as described herein. In some embodiments, the AAV is a self-complementary adeno-associated virus (scAAV), e.g., a scAAV that packages both strands which anneal together to form double stranded DNA. AAV serotypes that may be used in the disclosed methods include, e.g., AAV 1, AAV2, modified AAV2 (e.g., modifications at Y444F, Y500F, Y730F and/or S662V), AAV3, modified AAV3 (e.g., modifications at Y705F, Y731F and/or. T492V), AAV4, AAVS, AAV6, modified AAV6 (e.g., modifications at S663V and/or T492V), AAV8. AAV 8.2, AAV9, AAV rh 10, and pseudotyped AAV, such as AAV2/8, AAV2/5 and AAV2/6 can also be used in the disclosed methods.

In some embodiments, the Cas9- and/or gRNA-encoding DNA is delivered by a hybrid virus, e.g., a hybrid of one or more of the viruses described herein.

A Packaging cell is used to form a virus particle that is capable of infecting a host or target cell. Such a cell includes a 293 cell, which can package adenovirus, and a w2 cell or a PA317 cell, which can package retrovirus. A viral vector used in gene therapy is usually generated by a producer cell line that packages a nucleic acid vector into a viral particle. The vector typically contains the minimal viral sequences required for packaging and subsequent integration into a host or target cell (if applicable), with other viral sequences being replaced by an expression cassette encoding the protein to be expressed. For example, an AAV vector used in gene therapy typically only possesses inverted terminal repeat (ITR) sequences from the AAV genome which are required for packaging and gene expression in the host or target cell. The missing viral functions are supplied in trans by the packaging cell line. Henceforth, the viral DNA is packaged in a cell line, which contains a helper plasmid encoding the other AAV genes, namely rep and cap, but lacking ITR sequences. The cell line is also infected with adenovirus as a helper. The helper virus promotes replication of the AAV vector and expression of AAV genes from the helper plasmid. The helper plasmid is not packaged in significant amounts due to a lack of ITR sequences. Contamination with adenovirus can be reduced by, e.g., heat treatment to which adenovirus is more sensitive than AAV.

In an embodiment, the viral vector has the ability of cell type and/or tissue type recognition. For example, the viral vector can be pseudotyped with a different/alternative viral envelope glycoprotein; engineered with a cell type-specific receptor (e.g., genetic modification of the viral envelope glycoproteins to incorporate targeting ligands such as a peptide ligand, a single chain antibody, a growth factor); and/or engineered to have a molecular bridge with dual specificities with one end recognizing a viral glycoprotein and the other end recognizing a moiety of the target cell surface (e.g., ligand-receptor, monoclonal antibody, avidin-biotin and chemical conjugation).

In an embodiment, the viral vector achieves cell type specific expression. For example, a tissue-specific promoter can be constructed to restrict expression of the transgene (Cas 9 and gRNA) in only the target cell. The specificity of the vector can also be mediated by microRNA-dependent control of transgene expression. In an embodiment, the viral vector has increased efficiency of fusion of the viral vector and a target cell membrane. For example, a fusion protein such as fusion-competent hemagglutin (HA) can be incorporated to increase viral uptake into cells. In an embodiment, the viral vector has the ability of nuclear localization. For example, a virus that requires the breakdown of the cell wall (during cell division) and therefore will not infect a non-diving cell can be altered to incorporate a nuclear localization peptide in the matrix protein of the virus thereby enabling the transduction of non-proliferating cells.

In some embodiments, the Cas9- and/or gRNA-encoding DNA is delivered by a non-vector based method (e.g., using naked DNA or DNA complexes). For example, the DNA can be delivered, e.g., by organically modified silica or silicate (Ormosil), electroporation, gene gun, sonoporation, magnetofection, lipid-mediated transfection, dendrimers, inorganic nanoparticles, calcium phosphates, or a combination thereof.

In some embodiments, the Cas9- and/or gRNA-encoding DNA is delivered by a combination of a vector and a non-vector based method. For example, a virosome comprises a liposome combined with an inactivated virus (e.g., HIV or influenza virus), which can result in more efficient gene transfer, e.g., in a respiratory epithelial cell than either a viral or a liposomal method alone.

In an embodiment, the delivery vehicle is a non-viral vector. In an embodiment, the non-viral vector is an inorganic nanoparticle (e.g., attached to the payload to the surface of the nanoparticle).

Exemplary inorganic nanoparticles include, e.g., magnetic nanoparticles (e.g., Fe lvln0₂), or silica. The outer surface of the nanoparticle can be conjugated with a positively charged polymer (e.g., polyethylenimine, polylysine, polyserine) which allows for attachment (e.g., conjugation or entrapment) of payload. In an embodiment, the non-viral vector is an organic nanoparticle (e.g., entrapment of the payload inside the nanoparticle). Exemplary organic nanoparticles include, e.g., SNALP liposomes that contain cationic lipids together with neutral helper lipids which are coated with polyethylene glycol (PEG) and protamine and nucleic acid complex coated with lipid coating.

Exemplary lipids and/or polymers for for transfer of CRISPR systems or nucleic acid, e.g., vectors, encoding CRISPR systems or components thereof include, for example, those described in WO2011/076807, WO2014/136086, WO2005/060697, WO2014/140211, WO2012/031046, WO2013/103467, WO2013/006825, WO2012/006378, WO2015/095340, and WO2015/095346, the contents of each of the foregoing are hereby incorporated by reference in their entirety. In an embodiment, the vehicle has targeting modifications to increase target cell update of nanoparticles and liposomes, e.g., cell specific antigens, monoclonal antibodies, single chain antibodies, aptamers, polymers, sugars, and cell penetrating peptides. In an embodiment, the vehicle uses fusogenic and endosome-destabilizing peptides/polymers. In an embodiment, the vehicle undergoes acid-triggered conformational changes (e.g., to accelerate endosomal escape of the cargo). In an embodiment, a stimuli-cleavable polymer is used, e.g., for release in a cellular compartment. For example, disulfide-based cationic polymers that are cleaved in the reducing cellular environment can be used.

In an embodiment, the delivery vehicle is a biological non-viral delivery vehicle. In an embodiment, the vehicle is an attenuated bacterium (e.g., naturally or artificially engineered to be invasive but attenuated to prevent pathogenesis and expressing the transgene (e.g., Listeria monocytogenes, certain Salmonella strains, Bifidobacterium longum, and modified Escherichia coli), bacteria having nutritional and tissue-specific tropism to target specific tissues, bacteria having modified surface proteins to alter target tissue specificity). In an embodiment, the vehicle is a genetically modified bacteriophage (e.g., engineered phages having large packaging capacity, less immunogenic, containing mammalian plasmid maintenance sequences and having incorporated targeting ligands) In an embodiment, the vehicle is a mammalian virus-like particle. For example, modified viral particles can be generated (e.g., by purification of the “empty” particles followed by ex vivo assembly of the virus with the desired cargo). The vehicle can also be engineered to incorporate targeting ligands to alter target tissue specificity. In an embodiment, the vehicle is a biological liposome. For example, the biological liposome is a phospholipid-based particle derived from human cells (e.g., erythrocyte ghosts, which are red blood cells broken down into spherical structures derived from the subject (e.g., tissue targeting can be achieved by attachment of various tissue or cell-specific ligands), or secretory exosomes—subject (i.e., patient) derived membrane-bound nanovescicle (30-100 nm) of endocytic origin (e.g., can be produced from various cell types and can therefore be taken up by cells without the need of for targeting ligands).

In an embodiment, one or more nucleic acid molecules (e.g., DNA molecules) other than the components of a Cas system, e.g., the Cas9 molecule component and/or the gRNA molecule component described herein, are delivered. In an embodiment, the nucleic acid molecule is delivered at the same time as one or more of the components of the Cas system are delivered. In an embodiment, the nucleic acid molecule is delivered before or after (e.g., less than about 30 minutes, 1 hour, 2 hours, 3 hours, 6 hours, 9 hours, 12 hours, 1 day, 2 days, 3 days, 1 week, 2 weeks, or 4 weeks) one or more of the components of the Cas9 system are delivered. In an embodiment, the nucleic acid molecule is delivered by a different means than one or more of the components of the Cas9 system, e.g., the Cas9 molecule component and/or the gRNA molecule component, are delivered. The nucleic acid molecule can be delivered by any of the delivery methods described herein. For example, the nucleic acid molecule can be delivered by a viral vector, e.g., an integration-deficient lentivirus, and the Cas9 molecule component and/or the gRNA molecule component can be delivered by electroporation, e.g., such that the toxicity caused by nucleic acids (e.g., DNAs) can be reduced. In an embodiment, the nucleic acid molecule encodes a therapeutic protein, e.g., a protein described herein. In an embodiment, the nucleic acid molecule encodes an RNA molecule, e.g., an RNA molecule described herein. Delivery of RNA encoding a Cas9 molecule

RNA encoding Cas9 molecules (e.g., active Cas9 molecules, inactive Cas9 molecules or inactive Cas9 fusion proteins) and/or gRNA molecules, can be delivered into cells, e.g., target cells described herein, by art-known methods or as described herein. For example, Cas9-encoding and/or gRNA-encoding RNA can be delivered, e.g., by microinjection, electroporation, lipid-mediated transfection, peptide-mediated delivery, or a combination thereof.

Delivery of Cas9 Molecule as Protein

Cas9 molecules (e.g., active Cas9 molecules, inactive Cas9 molecules or inactive Cas9 fusion proteins) can be delivered into cells by art-known methods or as described herein. For example, Cas9 protein molecules can be delivered, e.g., by microinjection, electroporation, lipid-mediated transfection, peptide-mediated delivery, cell squeezing or abrasion (e.g., by nanoneedles) or a combination thereof. Delivery can be accompanied by DNA encoding a gRNA or by a gRNA, e.g., by precomplexing the gRNA and the Cas9 protein in a ribonuclear protein complex (RNP).

In an aspect the Cas9 molecule, e.g., as described herein, is delivered as a protein and the gRNA molecule is delivered as one or more RNAs (e.g., as a dgRNA or sgRNA, as described herein). In embodiments, the Cas9 protein is complexed with the gRNA molecule prior to delivery to a cell, e.g., as described herein, as a ribonuclear protein complex (“RNP”). In embodiments, the RNP can be delivered into cells, e.g., described herein, by any art-known method, e.g., electroporation. As described herein, and without being bound by theory, it can be preferable to use a gRNA moleucle and Cas9 molecule which result in high % editing at the target sequence (e.g., >85%, >90%, >95%, >98%, or >99%) in the target cell, e.g., described herein, even when the concentration of RNP delivered to the cell is reduced. Again, without being bound by theory, delivering a reduced or low concentration of RNP comprising a gRNA moleucle that produces a high % editing at the target sequence in the target cell (including at the low RNP concentration), can be beneficial because it may reduce the frequency and number of off-target editing events. In one aspect, where a low or reduced concentration of RNP is to be used, the following exemplary procedure can be used to generate the RNP with a dgRNA molecule:

-   -   1. Provide the Cas9 molecule and the tracr in solution at a high         concentration (e.g., a concentration higher than the final RNP         concentration to be delivered to the cell), and allow the two         components to equilibrate;     -   2. Provide the crRNA molecule, and allow the components to         equilibrate (thereby forming a high-concentration solution of         the RNP);     -   3. Dilute the RNP solution to the desired concentration;     -   4. Deliver said RNP at said desired concentration to the target         cells, e.g., by electroporation.

The above procedure may be modified for use with sgRNA molecules by omitting step 2, above, and in step 1, providing the Cas9 molecule and the sgRNA molecule in solution at high concentraiton, and allowing the components to equilibrate. In embodiments, the Cas9 moleucle and each gRNA component are provided in solution at a 1:2 ratio (Cas9:gRNA), e.g., a 1:2 molar ratio of Cas9:gRNA molecule. Where dgRNA molecules are used, the ratio, e.g., molar rato, is 1:2:2 (Cas9:tracr:crRNA). In embodiments, the RNP is formed at a concentration of 20 uM or higher, e.g., a concentration from about 20 uM to about 50 uM. In embodiments, the RNP is formed at a concentration of 10 uM or higher, e.g., a concentration from about 10 uM to about 30 uM. In embodiments, the RNP is diluted to a final concentration of 10 uM or less (e.g., a concentration from about 0.01 uM to about 10 uM) in a solution comprising the target cell (e.g., described herein) for delivery to said target cell. In embodiments, the RNP is diluted to a final concentration of 3 uM or less (e.g., a concentration from about 0.01 uM to about 3 uM) in a solution comprising the target cell (e.g., described herein) for delivery to said target cell. In embodiments, the RNP is diluted to a final concentration of 1 uM or less (e.g., a concentration from about 0.01 uM to about 1 uM) in a solution comprising the target cell (e.g., described herein) for delivery to said target cell. In embodiments, the RNP is diluted to a final concentration of 0.3 uM or less (e.g., a concentration from about 0.01 uM to about 0.3 uM) in a solution comprising the target cell (e.g., described herein) for delivery to said target cell. In embodiments, the RNP is provided at a final concentration of about 3 uM in a solution comprising the target cell (e.g., described herein) for delivery to said target cell. In embodiments, the RNP is provided at a final concentration of about 1 uM in a solution comprising the target cell (e.g., described herein) for delivery to said target cell. In embodiments, the RNP is provided at a final concentration of about 0.3 uM in a solution comprising the target cell (e.g., described herein) for delivery to said target cell. In embodiments, the RNP is provided at a final concentration of about 0.1 uM in a solution comprising the target cell (e.g., described herein) for delivery to said target cell. In embodiments, the RNP is provided at a final concentration of about 0.05 uM in a solution comprising the target cell (e.g., described herein) for delivery to said target cell. In embodiments, the RNP is provided at a final concentration of about 0.03 uM in a solution comprising the target cell (e.g., described herein) for delivery to said target cell. In embodiments, the RNP is provided at a final concentration of about 0.01 uM in a solution comprising the target cell (e.g., described herein) for delivery to said target cell. In embodiments, the RNP is formulated in a medium suitable for electroporation. In embodiments, the RNP is delivered to cells, e.g., HSPC cells, e.g., as described herein, by electroporation, e.g., using electroporation conditions described herein.

Bi-Modal or Differential Delivery of Components

Separate delivery of the components of a Cas system, e.g., the Cas9 molecule component and the gRNA molecule component, and more particularly, delivery of the components by differing modes, can enhance performance, e.g., by improving tissue specificity and safety.

In an embodiment, the Cas9 molecule and the gRNA molecule are delivered by different modes, or as sometimes referred to herein as differential modes. Different or differential modes, as used herein, refer modes of delivery that confer different pharmacodynamic or pharmacokinetic properties on the subject component molecule, e.g., a Cas9 molecule, gRNA molecule, or template nucleic acid. For example, the modes of delivery can result in different tissue distribution, different half-life, or different temporal distribution, e.g., in a selected compartment, tissue, or organ.

Some modes of delivery, e.g., delivery by a nucleic acid vector that persists in a cell, or in progeny of a cell, e.g., by autonomous replication or insertion into cellular nucleic acid, result-in more persistent expression of and presence of a component.

XI. Methods of Treatment

The Cas9 systems, e.g., one or more gRNA molecules and one or more Cas9 molecules, described herein are useful for the treatment of disease in a mammal, e.g., in a human. The terms “treat,” “treated,” “treating,” and “treatment,” include the administration of cas9 systems, e.g., one or more gRNA molecules and one or more cas9 molecules, to cells to prevent or delay the onset of the symptoms, complications, or biochemical indicia of a disease, alleviating the symptoms or arresting or inhibiting further development of the disease, condition, or disorder. Treatment may also include the administration of one or more (e.g., a population of) cells, e.g., HSPCs, that have been modified by the introduction of a gRNA molecule (or more than one gRNA molecule) of the present invention, or by the introduction of a CRISPR system as described herein, or by any of the methods of preparing said cells described herein, to prevent or delay the onset of the symptoms, complications, or biochemical indicia of a disease, alleviating the symptoms or arresting or inhibiting further development of the disease, condition, or disorder. Treatment may be prophylactic (to prevent or delay the onset of the disease, or to prevent the manifestation of clinical or subclinical symptoms thereof) or therapeutic suppression or alleviation of symptoms after the manifestation of the disease. Treatment can be measured by the therapeutic measures described hererin. Thus, the methods of “treatment” of the present invention also include administration of cells altered by the introduction of a cas9 system (e.g., one or more gRNA molecules and one or more Cas9 molecules) into said cells to a subject in order to cure, reduce the severity of, or ameliorate one or more symptoms of a disease or condition, in order to prolong the health or survival of a subject beyond that expected in the absence of such treatment. For example, “treatment” includes the alleviation of a disease symptom in a subject by at least 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or more.

Cas9 systems comprising gRNA molecules comprising the targeting domains described herein, e.g., in Tables 1, 2, 3, 4, 5, 6, 7, 8, and/or 9, are useful for the treatment of hemoglobinopathies.

Hemoglobinopathies

Hemoglobinopathies encompass a number of anemias of genetic origin in which there is a decreased production and/or increased destruction (hemolysis) of red blood cells (RBCs). These also include genetic defects that result in the production of abnormal hemoglobins with a concomitant impaired ability to maintain oxygen concentration. Some such disorders involve the failure to produce normal β-globin in sufficient amounts, while others involve the failure to produce normal β-globin entirely. These disorders associated with the β-globin protein are referred to generally as β-hemoglobinopathies. For example, β-thalassemias result from a partial or complete defect in the expression of the β-globin gene, leading to deficient or absent HbA. Sickle cell anemia results from a point mutation in the β-globin structural gene, leading to the production of an abnormal (sickle) hemoglobin (HbS). HbS is prone to polymerization, particularly under deoxygenated conditions. HbS RBCs are more fragile than normal RBCs and undergo hemolysis more readily, leading eventually to anemia.

In an embodiment, a genetic defect in alpha globin or beta globin is corrected, e.g., by homologous recombination, using the Cas9 molecules and gRNA molecules, e.g., CRISPR systems, described herein.

In an embodiment, a gene encoding a wild type (e.g., non-mutated) copy of alpha globin or beta globin is inserted into the genome of the cell, e.g., at a safe harbor site, e.g., at an AAVS1 safe harbor site, by homologous recombination, using a CRISPR system and methods described herein.

In an embodiment, a hemoglobinopathies-associated gene is targeted, using the Cas9 molecule and gRNA molecule described herein. Exemplary targets include, e.g., genes associated with control of the gamma-globin genes. In an embodiment, the target is BCL11A. In an embodiment, the target is a BCL11a enhancer. In an embodiment, the target is a HPFH region.

Fetal hemoglobin (also hemoglobin F or HbF or α2γ2) is a tetramer of two adult alpha-globin polypeptides and two fetal beta-like gamma-globin polypeptides. HbF is the main oxygen transport protein in the human fetus during the last seven months of development in the uterus and in the newborn until roughly 6 months old. Functionally, fetal hemoglobin differs most from adult hemoglobin in that it is able to bind oxygen with greater affinity than the adult form, giving the developing fetus better access to oxygen from the mother's bloodstream.

In newborns, fetal hemoglobin is nearly completely replaced by adult hemoglobin by approximately 6 months postnatally. In adults, fetal hemoglobin production can be reactivated pharmacologically, which is useful in the treatment of diseases such as hemoglobinopathies. For example, in certain patients with hemoglobinopathies, higher levels of gamma-globin expression can partially compensate for defective or impaired beta-globin gene production, which can ameliorate the clinical severity in these diseases. Increased HbF levels or F-cell (HbF containing erythrocyte) numbers can ameliorate the disease severity of hemoglobinopathies, e.g., beta-thalassemia major and sickle cell anemia.

Increased HbF levels or F-cell can be associated reduced BCL11A expression in cells. The BCL11A gene encodes a multi-zinc finger transcription factor. In an embodiment, the expression of BCL11A is modulated, e.g., down-regulated. In an embodiment, the BCL11A gene is edited. In an embodiment, the function of BCL11a, e.g., in an enrythroid lineage cell, is impaired or down-regulated. In an embodiment, the cell is a hemopoietic stem cell or progenitor cell.

Sickle Cell Diseases

Sickle cell disease is a group of disorders that affects hemoglobin. People with this disorder have atypical hemoglobin molecules (hemoglobin S), which can distort red blood cells into a sickle, or crescent, shape. Characteristic features of this disorder include a low number of red blood cells (anemia), repeated infections, and periodic episodes of pain.

Mutations in the HBB gene cause sickle cell disease. T e HBB gene provides instructions for making beta-globin. Various versions of beta-globin result from different mutations in the HBB gene. One particular HBB gene mutation produces an abnormal version of beta-globin known as hemoglobin S (HbS). Other mutations in the HBB gene lead to additional abnormal versions of beta-globin such as hemoglobin C (HbC) and hemoglobin E (HbE). HBB gene mutations can also result in an unusually low level of beta-globin, i.e., beta thalassemia.

In people with sickle cell disease, at least one of the beta-globin subunits in hemoglobin is replaced with hemoglobin S. In sickle cell anemia, which is a common form of sickle cell disease, hemoglobin S replaces both beta-globin subunits in hemoglobin. In other types of sickle cell disease, just one beta-globin subunit in hemoglobin is replaced with hemoglobin S. The other beta-globin subunit is replaced with a different abnormal variant, such as hemoglobin C. For example, people with sickle-hemoglobin C (HbSC) disease have hemoglobin molecules with hemoglobin S and hemoglobin C instead of beta-globin. If mutations that produce hemoglobin S and beta thalassemia occur together, individuals have hemoglobin S-beta thalassemia (HbSBetaThal) disease.

Beta Thalassemia

Beta thalassemia is a blood disorder that reduces the production of hemoglobin. In people with beta thalassemia, low levels of hemoglobin lead to a lack of oxygen in many parts of the body. Affected individuals also have a shortage of red blood cells (anemia), which can cause pale skin, weakness, fatigue, and more serious complications. People with beta thalassemia are at an increased risk of developing abnormal blood clots.

Beta thalassemia is classified into two types depending on the severity of symptoms: thalassemia major (also known as Cooley's anemia) and thalassemia intermedia. Of the two types, thalassemia major is more severe.

Mutations in the HBB gene cause beta thalassemia. The HBB gene provides instructions for making beta-globin. Some mutations in the HBB gene prevent the production of any beta-globin. The absence of beta-globin is referred to as beta-zero (Bº) thalassemia. Other HBB gene mutations allow some beta-globin to be produced but in reduced amounts, i.e., beta-plus (B⁺) thalassemia. People with both types have been diagnosed with thalassemia major and thalassemia intermedia.

In an embodiment, a Cas9 molecule/gRNA molecule complex targeting a first gene is used to treat a disorder characterized by second gene, e.g., a mutation in a second gene. By way of example, targeting of the first gene, e.g., by editing or payload delivery, can compensate for, or inhibit further damage from, the affect of a second gene, e.g., a mutant second gene. In an embodiment the allele(s) of the first gene carried by the subject is not causative of the disorder.

In one aspect, the invention relates to the treatment of a mammal, e.g., a human, in need of increased fetal hemoglobin (HbF).

In one aspect, the invention relates to the treatment of a mammal, e.g., a human, that has been diagnosed with, or is at risk of developing, a hemoglobinopathy.

In one aspect, the hemoglobinopathy is a β-hemoglobinopathy. In one aspect, the hemoglobinopathy is sickle cell disease. In one aspect, the hemoglobinopathy is beta thalassemia.

Methods of Treatment of Hemoglobinopathies

In another aspect the invention provides methods of treatment. In aspects, the gRNA molecules, CRISPR systems and/or cells of the invention are used to treat a patient in need thereof. In aspects, the patient is a mammal, e.g., a human. In aspects, the patient has a hemoglobinopathy. In embodiments, the patient has sickle cell disease. In embodiments, the patient has beta thalassemia.

In one aspect, the method of treatment comprises administering to a mammal, e.g., a human, one or more gRNA molecules, e.g., one or more gRNA molecules comprising a targeting domain described in Table 1, 2, 3, 4, 5, 6, 7, 8, or 9, and one or more cas9 molecules described herein.

In one aspect, the method of treatment comprises administering to a mammal a cell population, wherein the cell population is a cell population from a mammal, e.g., a human, that has been administered one or more gRNA molecules, e.g., one or more gRNA molecules comprising a targeting domain described in Table 1, 2, 3, 4, 5, 6, 7, 8, or 9, and one or more cas9 molecules described herein, e.g., a CRISPR system as described herein. In one embodiment, the administration of the one or more gRNA molecules or CRISPR systems to the cell is accomplished in vivo. In one embodiment the administration of the one or more gRNA molecules or CRISPR systems to the cell is accomplished ex vivo.

In one aspect, the method of treatment comprises administering to the mammal, e.g., the human, an effective amount of a cell population comprising cells which comprise or at one time comprised one or more gRNA molecules, e.g., one or more gRNA molecules comprising a targeting domain described in Table 1, 2, 3, 4, 5, 6, 7, 8, or 9, and one or more cas9 molecules described herein, or the progeny of said cells. In one embodiment, the cells are allogeneic to the mammal. In one embodiment, the cells are autologous to the mammal. In one embodiment the cells are harvested from the mammal, manipulated ex vivo, and returned to the mammal.

In aspects, the cells comprising or which at one time comprised one or more gRNA molecules, e.g., one or more gRNA molecules comprising a targeting domain described in Table 1, 2, 3, 4, 5, 6, 7, 8, or 9, and one or more cas9 molecules described herein, or the progeny of said cells, comprise stem cells or progenitor cells. In one aspect, the stem cells are hematopoietic stem cells. In one aspect, the progenitor cells are hematopoietic progenitor cells. In one aspect, the cells comprise both hematopoietic stem cells and hematopoietic progenitor cells, e.g., are HSPCs. In one aspect, the cells comprise, e.g., consist of, CD34+ cells. In one aspect the cells are substantially free of CD34− cells. In one aspect, the cells comprise, e.g., consist of, CD34+/CD90+ stem cells. In one aspect, the cells comprise, e.g., consist of, CD34+/CD90− cells. In an aspect, the cells are a population comprising one or more of the cell types described above or described herein.

In one embodiment, the disclosure provides a method for treating a hemoglobinopathy, e.g., sickle cell disease or beta-thalassemia, or a method for increasing fetal hemoglobin expression in a mammal, e.g., a human, in need thereof, the method comprising:

a) providing, e.g., harvesting or isolating, a population of HSPCs (e.g., CD34+ cells) from a mammal; b) providing said cells ex vivo, e.g., in a cell culture medium, optionally in the presence of an effective amount of a composition comprising at least one stem cell expander, whereby said population of HSPCs (e.g., CD34+ cells) expands to a greater degree than an untreated population; c) contacting the population of HSPCs (e.g., CD34+ cells) with an effective amount of: a composition comprising at least one gRNA molecule comprising a targeting domain described herein, e.g., a targeting domain described in Tables 1, 2, 3, 4, 5, 6, 7, 8, or 9, or a nucleic acid encoding said gRNA molecule, and at least one cas9 molecule, e.g., described herein, or a nucleic acid encoding said cas9 molecule, e.g., one or more RNPs as described herein, e.g., with a CRISPR system described herein; d) causing at least one modification in at least a portion of the cells of the population (e.g., at least a portion of the HSPCs, e.g., CD34+ cells, of the population), whereby, e.g., when said HSPCs are differentiated into cells of an erythroid lineage, e.g., red blood cells, fetal hemoglobin expression is increased, e.g., relative to cells not contacted according to step c); and f) returning a population of cells comprising said modified HSPCs (e.g., CD34+ cells) to the mammal.

In an aspect, the HSPCs are allogeneic to the mammal to which they are returned. In an aspect, the HSPCs are autologous to the mammal to which they are returned. In aspects, the HSPCs are isolated from bone marrow. In aspects, the HSPCs are isolated from peripheral blood, e.g., mobilized peripheral blood. In aspects, the moblized peripheral blood is isolated from a subject who has been administered a G-CSF. In aspects, the moblized peripheral blood is isolated from a subject who has been administered a moblization agent other than G-CSF, for example, Plerixafor® (AMD3100). In aspects, the HSPCs are isolated from umbilical cord blood.

In further embodiments of the method, the method further comprises, after providing a population of HSPCs (e.g., CD34+ cells), e.g., from a source described above, the step of enriching the population of cells for HSPCs (e.g., CD34+ cells). In embodiments of the method, after said enriching, the population of cells, e.g., HSPCs, is substantially free of CD34− cells.

In embodiments, the population of cells which is returned to the mammal includes at least 70% viable cells. In embodiments, the population of cells which is returned to the mammal includes at least 75% viable cells. In embodiments, the population of cells which is returned to the mammal includes at least 80% viable cells. In embodiments, the population of cells which is returned to the mammal includes at least 85% viable cells. In embodiments, the population of cells which is returned to the mammal includes at least 90% viable cells. In embodiments, the population of cells which is returned to the mammal includes at least 95% viable cells. In embodiments, the population of cells which is returned to the mammal includes at least 99% viable cells. Viability can be determined by staining a representative portion of the population of cells for a cell viability marker, e.g., as known in the art.

In another embodiment, the disclosure provides a method for treating a hemoglobinopathy, e.g., sickle cell disease or beta-thalassemia, or a method for increasing fetal hemoglobin expression in a mammal, e.g., a human, in need thereof, the method comprising the steps of:

a) providing, e.g., harvesting or isolating, a population of HSPCs (e.g., CD34+ cells) of a mammal, e.g., from the bone marrow of a mammal; b) isolating the CD34+ cells from the population of cells of step a); c) providing said CD34+ cells ex vivo, and culturing said cells, e.g., in a cell culture medium, in the presence of an effective amount of a composition comprising at least one stem cell expander, e.g., Compound 4, e.g., Compound 4 at a concentration of about 0.5 to about 0.75 micromolar, whereby said population of CD34+ cells expands to a greater degree than an untreated population; d) introducing into the cells of the population CD34+ cells an effective amount of: a composition comprising a Cas9 molecule, e.g., as described herein, and a gRNA molecule, e.g., as described herein, e.g., optionally where the Cas9 molecule and the gRNA molecule are in the form of an RNP, e.g., as described herein, and optionally where said introduction is by electroporation, e.g., as described herein, of said RNP into said cells; e) causing at least one genetic modification in at least a portion of the cells of the population (e.g., at least a portion of the HSPCs, e.g., CD34+ cells, of the population), whereby an indel, e.g., as described herein, is created at or near the genomic site complementary to the targeting domain of the gRNA introduced in step d); f) optionally, additionally culturing said cells after said introducing, e.g., in a cell culture medium, in the presence of an effective amount of a composition comprising at least one stem cell expander, e.g., Compound 4, e.g., Compound 4 at a concentration of about 0.5 to about 0.75 micromolar, such that the cells expand at least 2-fold, e.g., at least 4-fold, e.g., at least 5-fold; g) cryopreserving said cells; and h) returning the cells to the mammal, wherein,

-   -   the cells returned to the mammal comprise cells that 1) maintain         the ability to differentiate into cells of the erythroid         lineage, e.g., red blood cells; 2) when differentiated into red         blood cells, produce an increased level of fetal hemoglobin,         e.g., relative to cells unmodified by the gRNA of step e), e.g.,         produce at least 6 picograms fetal hemoglobin per cell.

In an aspect, the HSPCs are allogeneic to the mammal to which they are returned. In an aspect, the HSPCs are autologous to the mammal to which they are returned. In aspects, the HSPCs are isolated from bone marrow. In aspects, the HSPCs are isolated from peripheral blood, e.g., mobilized peripheral blood. In aspects, the moblized peripheral blood is isolated from a subject who has been administered a G-CSF. In aspects, the moblized peripheral blood is isolated from a subject who has been administered a moblization agent other than G-CSF, for example, Plerixafor® (AMD3100). In aspects, the HSPCs are isolated from umbilical cord blood.

In embodiments of the method above, the recited step b) results in a population of cells which is substantially free of CD34− cells.

In further embodiments of the method, the method further comprises, after providing a population of HSPCs (e.g., CD34+ cells), e.g., from a source described above, the population of cells is enriched for HSPCs (e.g., CD34+ cells).

In a further embodiments of these methods, the population of modified HSPCs (e.g., CD34+ stem cells) having the ability to differentiate increased fetal hemoglobin expression is cryopreserved and stored prior to being reintroduced into the mammal. In embodiments, the cryopreserved population of HSPCs having the ability to differentiate into cells of the erythroid lineage, e.g., red blood cells, and/or when differentiated into cells of the erythroid lineage, e.g., red blood cells, produce an increased level of fetal hemoglobin is thawed and then reintroduced into the mammal. In a further embodiment of these methods, the method comprises chemotherapy and/or radiation therapy to remove or reduce the endogenous hematopoietic progenitor or stem cells in the mammal. In a further embodiment of these methods, the method does not comprise a step of chemotherapy and/or radiation therapy to remove or reduce the endogenous hematopoietic progenitor or stem cells in the mammal. In a further embodiment of these methods, the method comprises a chemotherapy and/or radiation therapy to reduce partially (e.g., partial lymphodepletion) the endogenous hematopoietic progenitor or stem cells in the mammal. In embodiments the patient is treated with a fully lymphodepleting dose of busulfan prior to reintroduction of the modified HSPCs to the mammal. In embodiments, the patient is treated with a partially lymphodepleting dose of busulfan prior to reintroduction of the modified HSPCs to the mammal.

In embodiments, the cells are contacted with RNP comprising a Cas9 molecule, e.g., as described herein, complexed with a gRNA to the +58 BCL11a enhancer region. In embodiments, the gRNA comprises the targeting domain of CR000312. In embodiments, the gRNA comprises the targeting domain of CR000311. In embodiments, the gRNA comprises the targeting domain of CR001128. In embodiments, the gRNA comprises the targeting domain of CR001125. In embodiments, the gRNA comprises the targeting domain of CR001126. In embodiments, the gRNA comprises the targeting domain of CR001127. In embodiments the gRNA is a dual guide RNA comprising a crRNA comprising, e.g., consisting of, [SEQ ID NO: 248]-[SEQ ID NO: 6607], and a tracr comprising, e.g., consisting of, [SEQ ID NO: 7812], optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., SEQ ID NO: 6660. In embodiments, the gRNA is a sgRNA comprising, e.g., consisting of, [SEQ ID NO: 248]-[SEQ ID NO: 6601, optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., [SEQ ID NO: 248]-[SEQ ID NO: 7811]. In embodiments the gRNA is a dual guide RNA comprising a crRNA comprising, e.g., consisting of, [SEQ ID NO: 247]-[SEQ ID NO: 6607], and a tracr comprising, e.g., consisting of, SEQ ID NO: 7812, optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., SEQ ID NO: 6660. In embodiments, the gRNA is a sgRNA comprising, e.g., consisting of, [SEQ ID NO: 247]-[SEQ ID NO: 6601, optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., [SEQ ID NO: 247]-[SEQ ID NO: 7811]. In embodiments the gRNA is a dual guide RNA comprising a crRNA comprising, e.g., consisting of, [SEQ ID NO: 338]-[SEQ ID NO: 6607], and a tracr comprising, e.g., consisting of, SEQ ID NO: 7812, optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., SEQ ID NO: 6660. In embodiments, the gRNA is a sgRNA comprising, e.g., consisting of, [SEQ ID NO: 338]-[SEQ ID NO: 6601], optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., [SEQ ID NO: 338]-[SEQ ID NO: 7811]. In embodiments the gRNA is a dual guide RNA comprising a crRNA comprising, e.g., consisting of, [SEQ ID NO: 335]-[SEQ ID NO: 6607], and a tracr comprising, e.g., consisting of, SEQ ID NO: 7812, optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., SEQ ID NO: 6660. In embodiments, the gRNA is a sgRNA comprising, e.g., consisting of, [SEQ ID NO: 335]-[SEQ ID NO: 6601], optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., [SEQ ID NO: 335]-[SEQ ID NO: 7811]. In embodiments the gRNA is a dual guide RNA comprising a crRNA comprising, e.g., consisting of, [SEQ ID NO: 336]-[SEQ ID NO: 6607], and a tracr comprising, e.g., consisting of, SEQ ID NO: 7812, optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., SEQ ID NO: 6660. In embodiments, the gRNA is a sgRNA comprising, e.g., consisting of, [SEQ ID NO: 336]-[SEQ ID NO: 6601], optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., [SEQ ID NO: 336]-[SEQ ID NO: 7811]. In embodiments the gRNA is a dual guide RNA comprising a crRNA comprising, e.g., consisting of, [SEQ ID NO: 337]-[SEQ ID NO: 6607], and a tracr comprising, e.g., consisting of, SEQ ID NO: 7812, optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., SEQ ID NO: 6660. In embodiments, the gRNA is a sgRNA comprising, e.g., consisting of, [SEQ ID NO: 337]-[SEQ ID NO: 6601], optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., [SEQ ID NO: 337]-[SEQ ID NO: 7811]. In any of the aforementioned embodiments, any or all of the RNA components of the gRNA may be modified at one or more nucleotides, e.g., as described herein. In embodiments, the gRNA molecule is SEQ ID NO: 342. In embodiments, the gRNA molecule is SEQ ID NO: 343. In embodiments, the gRNA molecule is SEQ ID NO: 1762. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 344 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 344 and SEQ ID NO: 346. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 345 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 345 and SEQ ID NO: 346. In embodiments, the gRNA molecule is SEQ ID NO: 347. In embodiments, the gRNA molecule is SEQ ID NO: 348. In embodiments, the gRNA molecule is SEQ ID NO: 1763. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 349 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 349 and SEQ ID NO: 346. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 350 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 350 and SEQ ID NO: 346. In embodiments, the gRNA molecule is SEQ ID NO: 351. In embodiments, the gRNA molecule is SEQ ID NO: 352. In embodiments, the gRNA molecule is SEQ ID NO: 1764. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 353 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 353 and SEQ ID NO: 346. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 354 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 354 and SEQ ID NO: 346. In embodiments, the gRNA molecule is SEQ ID NO: 355. In embodiments, the gRNA molecule is SEQ ID NO: 356. In embodiments, the gRNA molecule is SEQ ID NO: 1765. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 357 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 357 and SEQ ID NO: 346. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 358 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 358 and SEQ ID NO: 346. In embodiments, the gRNA molecule is SEQ ID NO: 359. In embodiments, the gRNA molecule is SEQ ID NO: 360. In embodiments, the gRNA molecule is SEQ ID NO: 1766. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 361 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 361 and SEQ ID NO: 346. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 362 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 362 and SEQ ID NO: 346. In embodiments, the gRNA molecule is SEQ ID NO: 363. In embodiments, the gRNA molecule is SEQ ID NO: 364. In embodiments, the gRNA molecule is SEQ ID NO: 1767. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 365 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 365 and SEQ ID NO: 346. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 366 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 366 and SEQ ID NO: 346. In embodiments, the gRNA molecule is SEQ ID NO: 367. In embodiments, the gRNA molecule is SEQ ID NO: 368. In embodiments, the gRNA molecule is SEQ ID NO: 1768. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 369 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 369 and SEQ ID NO: 346. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 370 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 370 and SEQ ID NO: 346. In embodiments, the gRNA molecule is SEQ ID NO: 371. In embodiments, the gRNA molecule is SEQ ID NO: 372. In embodiments, the gRNA molecule is SEQ ID NO: 1769. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 373 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 373 and SEQ ID NO: 346. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 374 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 374 and SEQ ID NO: 346.

In embodiments, the cells are contacted with RNP comprising a Cas9 molecule, e.g., as described herein, complexed with a gRNA to the HPFH region. In embodiments, the gRNA comprises the targeting domain of CR001030. In embodiments, the gRNA comprises the targeting domain of CR001028. In embodiments, the gRNA comprises the targeting domain of CR001221. In embodiments, the gRNA comprises the targeting domain of CR001137. In embodiments, the gRNA comprises the targeting domain of CR003035. In embodiments, the gRNA comprises the targeting domain of CR003085. In embodiments the gRNA is a dual guide RNA comprising a crRNA comprising, e.g., consisting of, [SEQ ID NO: 98]-[SEQ ID NO: 6607], and a tracr comprising, e.g., consisting of, SEQ ID NO: 7812, optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., SEQ ID NO: 6660. In embodiments, the gRNA is a sgRNA comprising, e.g., consisting of, [SEQ ID NO: 98]-[SEQ ID NO: 6601], optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., [SEQ ID NO: 98]-[SEQ ID NO: 7811]. In embodiments the gRNA is a dual guide RNA comprising a crRNA comprising, e.g., consisting of, [SEQ ID NO: 100]-[SEQ ID NO: 6607], and a tracr comprising, e.g., consisting of, SEQ ID NO: 7812, optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., SEQ ID NO: 6660. In embodiments, the gRNA is a sgRNA comprising, e.g., consisting of, [SEQ ID NO: 100]-[SEQ ID NO: 6601], optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., [SEQ ID NO: 100]-[SEQ ID NO: 7811]. In embodiments the gRNA is a dual guide RNA comprising a crRNA comprising, e.g., consisting of, [SEQ ID NO: 1589]-[SEQ ID NO: 6607], and a tracr comprising, e.g., consisting of, SEQ ID NO: 7812, optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., SEQ ID NO: 6660. In embodiments, the gRNA is a sgRNA comprising, e.g., consisting of, [SEQ ID NO: 1589]-[SEQ ID NO: 6601], optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., [SEQ ID NO: 1589]-[SEQ ID NO: 7811]. In embodiments the gRNA is a dual guide RNA comprising a crRNA comprising, e.g., consisting of, [SEQ ID NO: 1505]-[SEQ ID NO: 6607], and a tracr comprising, e.g., consisting of, SEQ ID NO: 7812, optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., SEQ ID NO: 6660. In embodiments, the gRNA is a sgRNA comprising, e.g., consisting of, [SEQ ID NO: 1505]-[SEQ ID NO: 6601], optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., [SEQ ID NO: 1505]-[SEQ ID NO: 7811]. In embodiments the gRNA is a dual guide RNA comprising a crRNA comprising, e.g., consisting of, [SEQ ID NO: 1700]-[SEQ ID NO: 6607], and a tracr comprising, e.g., consisting of, SEQ ID NO: 7812, optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., SEQ ID NO: 6660. In embodiments, the gRNA is a sgRNA comprising, e.g., consisting of, [SEQ ID NO: 1700]-[SEQ ID NO: 6601], optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., [SEQ ID NO: 1700]-[SEQ ID NO: 7811]. In embodiments the gRNA is a dual guide RNA comprising a crRNA comprising, e.g., consisting of, [SEQ ID NO: 1750]-[SEQ ID NO: 6607], and a tracr comprising, e.g., consisting of, SEQ ID NO: 7812, optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., SEQ ID NO: 6660. In embodiments, the gRNA is a sgRNA comprising, e.g., consisting of, [SEQ ID NO: 1750]-[SEQ ID NO: 6601], optionally with 1, 2, 3, 4, 5, 6, or 7 additional 3′ uracil nucleotides, e.g., [SEQ ID NO: 1750]-[SEQ ID NO: 7811]. In embodiments, the gRNA molecule is SEQ ID NO: 375. In embodiments, the gRNA molecule is SEQ ID NO: 376. In embodiments, the gRNA molecule is SEQ ID NO: 1770. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 377 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 377 and SEQ ID NO: 346. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 378 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 378 and SEQ ID NO: 346. In embodiments, the gRNA molecule is SEQ ID NO: 379. In embodiments, the gRNA molecule is SEQ ID NO: 380. In embodiments, the gRNA molecule is SEQ ID NO: 1771. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 381 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 381 and SEQ ID NO: 346. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 382 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 382 and SEQ ID NO: 346. In embodiments, the gRNA molecule is SEQ ID NO: 383. In embodiments, the gRNA molecule is SEQ ID NO: 384. In embodiments, the gRNA molecule is SEQ ID NO: 1772. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 385 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 385 and SEQ ID NO: 346. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 386 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 386 and SEQ ID NO: 346. In embodiments, the gRNA molecule is SEQ ID NO: 387. In embodiments, the gRNA molecule is SEQ ID NO: 388. In embodiments, the gRNA molecule is SEQ ID NO: 1773. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 389 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 389 and SEQ ID NO: 346. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 390 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 390 and SEQ ID NO: 346. In embodiments, the gRNA molecule is SEQ ID NO: 391. In embodiments, the gRNA molecule is SEQ ID NO: 392. In embodiments, the gRNA molecule is SEQ ID NO: 1774. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 393 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 393 and SEQ ID NO: 346. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 394 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 394 and SEQ ID NO: 346. In embodiments, the gRNA molecule is SEQ ID NO: 395. In embodiments, the gRNA molecule is SEQ ID NO: 396. In embodiments, the gRNA molecule is SEQ ID NO: 1775. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 397 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 397 and SEQ ID NO: 346. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 398 and SEQ ID NO: 6660. In embodiments the gRNA molecule is a dgRNA molecule that consists of SEQ ID NO: 398 and SEQ ID NO: 346.

In embodiments, the stem cell expander is Compound 1. In embodiments, the stem cell expander is Compound 2. In embodiments, the stem cell expander is Compound 3. In embodiments, the stem cell expander is Compound 4. In embodiments, the stem cell expander is Compound 4 and is present at a concentration of 2-0.1 micromolar, e.g., 1-0.25 micromolar, e.g., 0.75-0.5 micromolar. In embodiments, the stem cell expander is a molecule described in WO2010/059401 (e.g., the molecule described in Example 1 of WO2010/059401).

In embodiments, the cells, e.g., HSPCs, e.g., as described herein, are cultured ex vivo for a period of about 1 hour to about 15 days, e.g., a period of about 12 hours to about 12 days, e.g., a period of about 12 hours to 4 days, e.g., a period of about 1 day to about 4 days, e.g., a period of about 1 day to about 2 days, e.g., a period of about 1 day or a period of about 2 days, prior to the step of contacting the cells with a CRISPR system, e.g., described herein. In embodiments, said culturing prior to said contacting step is in a composition (e.g., a cell culture medium) comprising a stem cell expander, e.g., described herein, e.g., compound 4, e.g., compound 4 at a concentration of about 0.25 uM to about 1 uM, e.g., compound 4 at a concentration of about 0.75-0.5 micromolar. In embodiments, the cells are cultured ex vivo for a period of no more than about about 1 day, e.g., no more than about 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 hour(s) after the step of contacting the cells with a CRISPR system, e.g., described herein, e.g., in a cell culture medium which comprises a stem cell expander, e.g., described herein, e.g., compound 4, e.g., compound 4 at a concentration of about 0.25 uM to about 1 uM, e.g., compound 4 at a concentration of about 0.75-0.5 micromolar. In other embodiments, the cells are cultured ex vivo for a period of about 1 hour to about 15 days, e.g., a period of about 12 hours to about 10 days, e.g., a period of about 1 day to about 10 days, e.g., a period of about 1 day to about 5 days, e.g., a period of about 1 thy to about 4 days, e.g., a period of about 2 days to about 4 days, e.g., a period of about 2 days, about 3 days or about 4 days, after the step of contacting the cells with a CRISPR system, e.g., described herein, in a cell culture medium, e.g., which comprises a stem cell expander, e.g., described herein, e.g., compound 4, e.g., compound 4 at a concentration of about 0.25 uM to about 1 uM, e.g., compound 4 at a concentration of about 0.75-0.5 micromolar. In embodiments, the cells are cultured ex vivo (e.g., cultured prior to said contacting step and/or cultured after said contacting step) for a period of about 1 hour to about 20 days, e.g., a period of about 6-12 days, e.g., a period of about 6, about 7, about 8, about 9, about 10, about 11, or about 12 days.

In embodiments, the population of cells comprising the modified HSPCs returned to the mammal comprises at least about 1 million cells (e.g., at least about 1 million CD34+ cells) per kg. In embodiments, the population of cells comprising the modified HSPCs returned to the mammal comprises at least about 2 million cells (e.g., at least about 2 million CD34+ cells) per kg. In embodiments, the population of cells comprising the modified HSPCs returned to the mammal comprises at least about 3 million cells (e.g., at least about 3 million CD34+ cells) per kg. In embodiments, the population of cells comprising the modified HSPCs returned to the mammal comprises at least about 4 million cells (e.g., at least about 4 million CD34+ cells) per kg. In embodiments, the population of cells comprising the modified HSPCs returned to the mammal comprises at least about 5 million cells (e.g., at least about 5 million CD34+ cells) per kg. In embodiments, the population of cells comprising the modified HSPCs returned to the mammal comprises at least about 6 million cells (e.g., at least about 6 million CD34+ cells) per kg. In embodiments, the population of cells comprising the modified HSPCs returned to the mammal comprises at least 1 million cells (e.g., at least 1 million CD34+ cells) per kg. In embodiments, the population of cells comprising the modified HSPCs returned to the mammal comprises at least 2 million cells (e.g., at least 2 million CD34+ cells) per kg. In embodiments, the population of cells comprising the modified HSPCs returned to the mammal comprises at least 3 million cells (e.g., at least 3 million CD34+ cells) per kg. In embodiments, the population of cells comprising the modified HSPCs returned to the mammal comprises at least 4 million cells (e.g., at least 4 million CD34+ cells) per kg. In embodiments, the population of cells comprising the modified HSPCs returned to the mammal comprises at least 5 million cells (e.g., at least 5 million CD34+ cells) per kg. In embodiments, the population of cells comprising the modified HSPCs returned to the mammal comprises at least 6 million cells (e.g., at least 6 million CD34+ cells) per kg. In embodiments, the population of cells comprising the modified HSPCs returned to the mammal comprises about 1 million cells (e.g., about 1 million CD34+ cells) per kg. In embodiments, the population of cells comprising the modified HSPCs returned to the mammal comprises about 2 million cells (e.g., about 2 million CD34+ cells) per kg. In embodiments, the population of cells comprising the modified HSPCs returned to the mammal comprises about 3 million cells (e.g., about 3 million CD34+ cells) per kg. In embodiments, the population of cells comprising the modified HSPCs returned to the mammal comprises about 4 million cells (e.g., about 4 million CD34+ cells) per kg. In embodiments, the population of cells comprising the modified HSPCs returned to the mammal comprises about 5 million cells (e.g., about 5 million CD34+ cells) per kg. In embodiments, the population of cells comprising the modified HSPCs returned to the mammal comprises about 6 million cells (e.g., about 6 million CD34+ cells) per kg. In embodiments, the population of cells comprising the modified HSPCs returned to the mammal comprises about 2×10⁶ cells per kg body weight of the patient. In embodiments, the population of cells comprising the modified HSPCs returned to the mammal comprises at least 2×10⁶ cells per kg body weight of the patient.

In embodiments, any of the methods described above results in the patient having at least 80% of its circulating CD34+ cells comprising an indel at or near the genomic site complementary to the targeting domain of the gRNA molecule used in the method, e.g., as measured at least 15 days, e.g., at least 20, at least 30, at least 40 at least 50 or at least 60 days after reintroduction of the cells into the mammal.

In embodiments, any of the methods described above results in the patient having at least 20% of its bone marrow CD34+ cells comprising an indel at or near the genomic site complementary to the targeting domain of the gRNA molecule used in the method, e.g., as measured at least 15 days, e.g., at least 20, at least 30, at least 40 at least 50 or at least 60 days after reintroduction of the cells into the mammal.

In embodiments, the HSPCs that are reintroduced into the mammal are able to differentiate in vivo into cells of the erythroid lineage, e.g., red blood cells, and said differentiated cells exhibit increased fetal hemoglobin levels, e.g., produce at least 6 picograms fetal hemoglobin per cell, e.g., at least 7 picograms fetal hemoglobin per cell, at least 8 picograms fetal hemoglobin per cell, at least 9 picograms fetal hemoglobin per cell, at least 10 picograms fetal hemoglobin per cell, e.g., between about 9 and about 10 picograms fetal hemoglobin per cell, e.g., such that the hemoglobinopathy is treated the mammal.

It will be understood that when a cell is characterized as having increased fetal hemoglobin, that includes embodiments in which a progeny, e.g., a differentiated progeny, of that cell exhibits increased fetal hemoglobin. For example, in the methods described herein, the altered or modified CD34+ cell (or cell population) may not express increased fetal hemoglobin, but when differentiated into cells of erythroid lineage, e.g., red blood cells, the cells express increased fetal hemoglobin, e.g., increased fetal hemoglobin relative to an unmodified or unaltered cell under similar conditions.

XII. Culture Methods and Methods of Manufacturing Cells

The disclosure provides methods of culturing cells, e.g., HSPCs, e.g., hematopoietic stem cells, e.g., CD34+ cells modified, or to be modified, with the gRNA molecules described herein.

DNA Repair Pathway Inhibitors

Without being bound by theory, it is believed that the pattern of indels produced by a given gRNA molecule at a particular target sequence is a product of each of the active DNA repair mechamisms within the cell (e.g., non-homologous end joining, microhomology-mediated end joining, etc.). Wihtout being bound by theory, it is believed that a particularly favorable indel may be selected for or enriched for by contacting the cells to be edited with an inhibitor of a DNA repair pathway that does not produce the desired indel. Thus, the gRNA molecules, CRISPR systems, methods and other aspects of the invention may be performed in combination with such inhibitors. Examples of such inhibitors include those described in, e.g., WO2014/130955, the contents of which are hereby incorporated by reference in their entirety. In embodiment, the inhibitor is a DNAPKc inhibitor, e.g., NU7441.

Stem Cell Expanders

In one aspect the invention relates to culturing the cells, e.g., HSPCs, e.g., CD34+ cells modified, or to be modified, with the gRNA molecules described herein, with one or more agents that result in an increased expansion rate, increased expansion level, or increased engraftment relative to cells not treated with the agent. Such agents are referred to herein as stem cell expanders.

In an aspect, the one or more agents that result in an increased expansion rate or increased expansion level, relative to cells not treated with the agent, e.g., the stem cell expander, comprises an agent that is an inhibitor of the aryl hydrocarbon receptor (AHR) pathway. In aspects, the stem cell expander is a compound disclosed in WO2013/110198 or a compound disclosed in WO2010/059401, the contents of which are incorporated by reference in their entirety.

In one aspect, the one or more agents that result in an increased expansion rate or increased expansion level, relative to cells not treated with the agent, is a pyrimido[4,5-b]indole derivative, e.g., as disclosed in WO2013/110198, the contents of which are hereby incorporated by reference in their entirety. In one embodiment the agent is compound 1 ((1r,4r)-N¹-(2-benzyl-7-(2-methyl-2H-tetrazol-5-yl)-9H-pyrimido[4,5-b]indol-4-yl)cyclohexane-1,4-diamine):

Compound 1

In another aspect, the agent is Compound 2 (methyl 4-(3-piperidin-1-ylpropylamino)-9H-pyrimido[4,5-b]indole-7-carboxylate):

Compound 2:

In another aspect, the one or more agents that result in an increased expansion rate or increased expansion level, relative to cells not treated with the agent, is an agent disclosed in WO2010/059401, the contents of which are hereby incorporated by reference in their entirety.

In one embodiment, the stem cell expander is 4-(2-(2-(benzo[b]thiophen-3-yl)-9-isopropyl-9H-purin-6-ylamino)ethyl)phenol, i.e., is the compound from example 1 of WO2010/059401, having the following structure:

Compound 3:

In another aspect, the stem cell expander is compound 4 ((S)-2-(6-(2-(1H-indol-3-yl)ethylamino)-2-(5-fluoropyridin-3-yl)-9H-purin-9-yl)propan-1-ol, i.e., is the compound 157S according to WO2010/059401), having the following structure:

Compound 4:

In embodiments the population of HSPCs is contacted with the stem cell expander, e.g., compound 1, compound 2, compound 3, compound 4, or combinations thereof (e.g., a combination of compound 1 and compound 4) before introduction of the CRISPR system (e.g., gRNA molecule and/or Cas9 molecule of the invention) to said HSPCs. In embodiments, the population of HSPCs is contacted with the stem cell expander, e.g., compound 1, compound 2, compound 3, compound 4, or combinations thereof (e.g., a combination of compound 1 and compound 4), after introduction of the CRISPR system (e.g., gRNA molecule and/or Cas9 molecule of the invention) to said HSPCs. In embodiments, the population of HSPCs is contacted with the stem cell expander, e.g., compound 1, compound 2, compound 3, compound 4, or combinations thereof (e.g., a combination of compound 1 and compound 4), both before and after introduction of the CRISPR system (e.g., gRNA molecule and/or Cas9 molecule of the invention) to said HSPCs.

In embodiments, the stem cell expander is present in an effective amount to increase the expansion level of the HSPCs, relative to HSPCs in the same media but for the absence of the stem cell expander. In embodiments, the stem cell expander is present at a concentration ranging from about 0.01 to about 10 uM, e.g., from about 0.1 uM to about 1 uM. In embodiments, the stem cell expander is present in the cell culture medium at a concentration of about 1 uM, about 950 nM, about 900 nM, about 850 nM, about 800 nM, about 750 nM, about 700 nM, about 650 nM, about 600 nM, about 550 nM, about 500 nM, about 450 nM, about 400 nM, about 350 nM, about 300 nM, about 250 nM, about 200 nM, about 150 nM, about 100 nM, about 50 nM, about 25 nM, or about 10 nM. In embodiments, the stem cell expander is present at a concentration ranging from about 500 nM to about 750 nM.

In embodiments, the stem cell expander is compound 4, which is present in the cell culture medium at a concentration ranging from about 0.01 to about 10 micromolar (uM). In embodiments, the stem cell expander is compound 4, which is present in the cell culture medium at a concentration ranging from about 0.1 to about 1 micromolar (uM). In embodiments, the stem cell expander is compound 4, which is present in the cell culture medium at a concentration of about 0.75 micromolar (uM). In embodiments, the stem cell expander is compound 4, which is present in the cell culture medium at a concentration of about 0.5 micromolar (uM). In embodiments of any of the foregoing, the cell culture medium additionally comprises compound 1.

In embodiments, the stem cell expander is a mixture of compound 1 and compound 4.

In embodiments, the cells of the invention are contacted with one or more stem cell expander molecules for a sufficient time and in a sufficient amount to cause a 2 to 10,000-fold expansion of CD34+ cells, e.g., a 2-1000-fold expansion of CD34+ cells, e.g., a 2-100-fold expansion of CD34+ cells, e.g., a 20-200-fold expansion of CD34+ cells. As described herein, the contacting with the one or more stem cell expanders may be before the cells are contacted with a CRISPR system, e.g., as described herein, after the cells are contacted with a CRISPR system, e.g., as described herein, or a combination thereof. In an embodiment, the cells are contacted with one or more stem cell expander molecules, e.g., Compound 4, for a sufficient time and in a sufficient amount to cause at least a 2-fold expansion of CD34+ cells, e.g., CD34+ cells comprising an indel at or near the target site having complementarity to the targeting domain of the gRNA of the CRISPR/Cas9 system introduced into said cell. In an embodiment, the cells are contacted with one or more stem cell expander molecules, e.g., Compound 4, for a sufficient time and in a sufficient amount to cause at least a 4-fold expansion of CD34+ cells, e.g., CD34+ cells comprising an indel at or near the target site having complementarity to the targeting domain of the gRNA of the CRISPR/Cas9 system introduced into said cell. In an embodiment, the cells are contacted with one or more stem cell expander molecules, e.g., Compound 4, for a sufficient time and in a sufficient amount to cause at least a 5-fold expansion of CD34+ cells, e.g., CD34+ cells comprising an indel at or near the target site having complementarity to the targeting domain of the gRNA of the CRISPR/Cas9 system introduced into said cell. In an embodiment, the cells are contacted with one or more stem cell expander molecules for a sufficient time and in a sufficient amount to cause at least a 10-fold expansion of CD34+ cells. In an embodiment, the cells are contacted with one or more stem cell expander molecules for a sufficient time and in a sufficient amount to cause at least a 20-fold expansion of CD34+ cells. In an embodiment, the cells are contacted with one or more stem cell expander molecules for a sufficient time and in a sufficient amount to cause at least a 30-fold expansion of CD34+ cells. In an embodiment, the cells are contacted with one or more stem cell expander molecules for a sufficient time and in a sufficient amount to cause at least a 40-fold expansion of CD34+ cells. In an embodiment, the cells are contacted with one or more stem cell expander molecules for a sufficient time and in a sufficient amount to cause at least a 50-fold expansion of CD34+ cells. In an embodiment, the cells are contacted with one or more stem cell expander molecules for a sufficient time and in a sufficient amount to cause at least a 60-fold expansion of CD34+ cells. In embodiments, the cells are contacted with the one or more stem cell expanders for a period of about 1-60 days, e.g., about 1-50 days, e.g., about 1-40 days, e.g., about 1-30 days, e.g., 1-20 days, e.g., about 1-10 days, e.g., about 7 days, e.g., about 1-5 days, e.g., about 2-5 days, e.g., about 2-4 days, e.g., about 2 days or, e.g., about 4 days.

In embodiments, the cells, e.g., HSPCs, e.g., as described herein, are cultured ex vivo for a period of about 1 hour to about 10 days, e.g., a period of about 12 hours to about 5 days, e.g., a period of about 12 hours to 4 days, e.g., a period of about 1 day to about 4 days, e.g., a period of about 1 day to about 2 days, e.g., a period of about 1 day or a period of about 2 days, prior to the step of contacting the cells with a CRISPR system, e.g., described herein. In embodiments, said culturing prior to said contacting step is in a composition (e.g., a cell culture medium) comprising a stem cell expander, e.g., described herein, e.g., compound 4, e.g., compound 4 at a concentration of about 0.25 uM to about 1 uM, e.g., compound 4 at a concentration of about 0.75-0.5 micromolar. In embodiments, the cells are cultured ex vivo for a period of no more than about about 1 day, e.g., no more than about 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 hour(s) after the step of contacting the cells with a CRISPR system, e.g., described herein, e.g., in a cell culture medium which comprises a stem cell expander, e.g., described herein, e.g., compound 4, e.g., compound 4 at a concentration of about 0.25 uM to about 1 uM, e.g., compound 4 at a concentration of about 0.75-0.5 micromolar. In other embodiments, the cells are cultured ex vivo for a period of about 1 hour to about 14 days, e.g., a period of about 12 hours to about 10 days, e.g., a period of about 1 day to about 10 days, e.g., a period of about 1 day to about 5 days, e.g., a period of about 1 day to about 4 days, e.g., a period of about 2 days to about 4 days, e.g., a period of about 2 days, about 3 days or about 4 days, after the step of contacting the cells with a CRISPR system, e.g., described herein, in a cell culture medium, e.g., which comprises a stem cell expander, e.g., described herein, e.g., compound 4, e.g., compound 4 at a concentration of about 0.25 uM to about 1 uM, e.g., compound 4 at a concentration of about 0.75-0.5 micromolar.

In embodiments, the cell culture medium is a chemically defined medium. In embodiments, the cell culture medium may additionally contain, for example, StemSpan SFEM (StemCell Technologies; Cat no. 09650). In embodiments, the cell culture medium may alternatively or additionally contain, for example, HSC Brew, GMP (Miltenyi). In embodiments, the media may be supplemented with thrombopoietin (TPO), human Flt3 ligand (Flt-3L), human stem cell factor (SCF), human interleukin-6, L-glutamine, and/or penicillin/streptomycin. In embodiments, the media is supplemented with thrombopoietin (TPO), human Flt3 ligand (Flt-3L), human stem cell factor (SCF), human interleukin-6, and L-glutamine. In other embodiments, the media is supplemented with thrombopoietin (TPO), human Flt3 ligand (Flt-3L), human stem cell factor (SCF), and human interleukin-6. In other embodiments the media is supplemented with thrombopoietin (TPO), human Flt3 ligand (Flt-3L), and human stem cell factor (SCF), but not human interleukin-6. When present in the medium, the thrombopoietin (TPO), human Flt3 ligand (Flt-3L), human stem cell factor (SCF), human interleukin-6, and/or L-glutamine are each present in a concentration ranging from about 1 ng/mL to about 1000 ng/mL, e.g., a concentration ranging from about 10 ng/mL to about 500 ng/mL, e.g., a concentration ranging from about 10 ng/mL to about 100 ng/mL, e.g., a concentration ranging from about 25 ng/mL to about 75 ng/mL, e.g., a concentration of about 50 ng/mL. In embodiments, each of the supplemented components is at the same concentration. In other embodiments, each of the supplemented components is at a different concentration. In an embodiment, the medium comprises StemSpan SFEM (StemCell Technologies; Cat no. 09650), 50 ng/mL of thrombopoietin (Tpo), 50 ng/mL of human Flt3 ligand (Flt-3L), 50 ng/mL of human stem cell factor (SCF), and 50 ng/mL of human interleukin-6 (IL-6). In an embodiment, the medium comprises StemSpan SFEM (StemCell Technologies; Cat no. 09650), 50 ng/mL of thrombopoietin (Tpo), 50 ng/mL of human Flt3 ligand (Flt-3L), and 50 ng/mL of human stem cell factor (SCF), and does not comprise IL-6. In embodiments, the media further comprises a stem cell expander, e.g., compound 4, e.g., compound 4 at a concentration of 0.75 μM. In embodiments, the media further comprises a stem cell expander, e.g., compound 4, e.g., compound 4 at a concentration of 0.5 μM. In embodiments, the media further comprises 1% L-glutamine and 2% penicillin/streptomycin. In embodiments, the cell culture medium is serum free.

XII. Combination Therapy

The present disclosure contemplates the use of the gRNA molecules described herein, or cells (e.g., hematopoietic stem cells, e.g., CD34+ cells) modified with the gRNA molecules described herein, in combination with one or more other therapeutic modalities and/or agents agents. Thus, in addition to the use of the gRNA molecules or cells modified with the gRNA molecules described herein, one may also administer to the subject one or more “standard” therapies for treating hemoglobinopathies.

The one or more additional therapies for treating hemoglobinopathies may include, for example, additional stem cell transplantation, e.g., hematopoietic stem cell transplantation. The stem cell transplantation may be allogeneic or autologous.

The one or more additional therapies for treating hemoglobinopathies may include, for example, blood transfusion and/or iron chealation (e.g., removal) therapy. Known iron chealation agents include, for example, deferoxamine and deferasirox.

The one or more additional therapies for treating hemoglobinopathies may include, for example, folic acid supplements, or hydroxyurea (e.g., 5-hydroxyurea). The one or more additional therapies for treating hemoglobinopathies may be hydroxyurea. In embodiments, the hydroxyurea may be administered at a dose of, for example, 10-35 mg/kg per day, e.g., 10-20 mg/kg per day. In embodiments, the hydroxyurea is adminstered at a dose of 10 mg/kg per day. In embodiments, the hydroxyurea is adminstered at a dose of 10 mg/kg per day. In embodiments, the hydroxyurea is adminstered at a dose of 20 mg/kg per day. In embodiments, the hydroxyurea is administered before and/or after the cell (or population of cells), e.g., CD34+ cell (or population of cells) of the invention, e.g., as described herein.

The one or more additional therapeutic agents may include, for example, an anti-p-selectin antibody, e.g., SelG1 (Selexys). P-selectin antibodies are described in, for example, PCT publication WO1993/021956, PCT publication WO1995/034324, PCT publication WO2005/100402, PCT publication WO2008/069999, US patent application publication US2011/0293617, U.S. Pat. No. 5,800,815, U.S. Pat. No. 6,667,036, U.S. Pat. No. 8,945,565, U.S. Pat. No. 8,377,440 and U.S. Pat. No. 9,068,001, the contents of each of which are incorporated herein in their entirety.

The one or more additional agents may include, for example, a small molecule which upregulates fetal hemoglobin. Examples of such molecules include TN1 (e.g., as described in Nam, T. et al., ChemMedChem 2011, 6, 777-780, DOI: 10.1002/cmdc.201000505, herein incorporated by reference).

The one or more additional therapies may also include irradiation or other bone marrow ablation therapies known in the art. An example of such a therapy is busulfan. Such additional therapy may be performed prior to introduction of the cells of the invention into the subject. In an embodiment the methods of treatment described herein (e.g., the methods of treatment that include administration of cells (e.g., HSPCs) modified by the methods described herein (e.g., modified with a CRISPR system described herein, e.g., to increase HbF production)), the method does not include the step of bone marrow ablation. In embodiments, the methods include a partial bone marrow ablation step.

The therapies described herein (e.g., comprising administering a population of HSPCs, e.g., HSPCs modified using a CRISPR system described herein) may also be combined with an additional therapeutic agent. In an embodiment, the additional therapeutic agent is an HDAC inhibitor, e.g., panobinostat. In an embodiment, the additional therapeutic is a compound described in PCT Publication No. WO2014/150256, e.g., a compound described in Table 1 of WO2014/150256, e.g., GBT440. Other examples of HDAC inhibitors include, for example, suberoylanilide hydroxamic acid (SAHA). The one or more additional agents may include, for example, a DNA methylation inhibitor. Such agents have been shown to increase the HbF induction in cells having reduced BCL11a activity (e.g., Jian Xu et al, Science 334, 993 (2011); DOI: 0.1126/science.1211053, herein incorporated by reference). Other HDAC inhibitors include any HDAC inhibitor known in the art, for example, trichostatin A, HC toxin, DACI-2, FK228, DACI-14, depudicin, DACI-16, tubacin, NK57, MAZ1536, NK125, Scriptaid, Pyroxamide, MS-275, ITF-2357, MCG-D0103, CRA-024781, CI-994, and LBH589 (see, e.g., Bradner J E, et al., PNAS, 2010 (vol. 107:28), 12617-12622, herein incorporated by reference in its entirety).

The gRNA molecules described herein, or cells (e.g., hematopoietic stem cells, e.g., CD34+ cells) modified with the gRNA molecules described herein, and the co-therapeutic agent or co-therapy can be administered in the same formulation or separately. In the case of separate administration, the gRNA molecules described herein, or cells modified with the gRNA molecules described herein, can be administered before, after or concurrently with the co-therapeutic or co-therapy. One agent may precede or follow administration of the other agent by intervals ranging from minutes to weeks. In embodiments where two or more different kinds of therapeutic agents are applied separately to a subject, one would generally ensure that a significant period of time did not expire between the time of each delivery, such that these different kinds of agents would still be able to exert an advantageously combined effect on the target tissues or cells.

XIII. Modified Nucleosides, Nucleotides, and Nucleic Acids

Modified nucleosides and modified nucleotides can be present in nucleic acids, e.g., particularly gRNA, but also other forms of RNA, e.g., mRNA, RNAi, or siRNA. As described herein “nucleoside” is defined as a compound containing a five-carbon sugar molecule (a pentose or ribose) or derivative thereof, and an organic base, purine or pyrimidine, or a derivative thereof. As described herein, “nucleotide” is defined as a nucleoside further comprising a phosphate group.

Modified nucleosides and nucleotides can include one or more of:

(i) alteration, e.g., replacement, of one or both of the non-linking phosphate oxygens and/or of one or more of the linking phosphate oxygens in the phosphodiester backbone linkage; (ii) alteration, e.g., replacement, of a constituent of the ribose sugar, e.g., of the 2′ hydroxyl on the ribose sugar; (iii) wholesale replacement of the phosphate moiety with “dephospho” linkers; (iv) modification or replacement of a naturally occurring nucleobase, including with a non-canonical nucleobase; (v) replacement or modification of the ribose-phosphate backbone; (vi) modification of the 3′ end or 5′ end of the oligonucleotide, e.g., removal, modification or replacement of a terminal phosphate group or conjugation of a moiety, cap or linker; and (vii) modification or replacement of the sugar.

The modifications listed above can be combined to provide modified nucleosides and nucleotides that can have two, three, four, or more modifications. For example, a modified nucleoside or nucleotide can have a modified sugar and a modified nucleobase. In an embodiment, every base of a gRNA is modified, e.g., all bases have a modified phosphate group, e.g., all are phosphorothioate groups. In an embodiment, all, or substantially all, of the phosphate groups of a unimolecular or modular gRNA molecule are replaced with phosphorothioate groups. In embodiments, one or more of the five 3′-terminal bases and/or one or more of the five 5′-terminal bases of the gRNA are modified with a phosphorothioate group.

In an embodiment, modified nucleotides, e.g., nucleotides having modifications as described herein, can be incorporated into a nucleic acid, e.g., a “modified nucleic acid.” In some embodiments, the modified nucleic acids comprise one, two, three or more modified nucleotides. In some embodiments, at least 5% (e.g., at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or about 100%) of the positions in a modified nucleic acid are a modified nucleotides.

Unmodified nucleic acids can be prone to degradation by, e.g., cellular nucleases. For example, nucleases can hydrolyze nucleic acid phosphodiester bonds. Accordingly, in one aspect the modified nucleic acids described herein can contain one or more modified nucleosides or nucleotides, e.g., to introduce stability toward nucleases.

In some embodiments, the modified nucleosides, modified nucleotides, and modified nucleic acids described herein can exhibit a reduced innate immune response when introduced into a population of cells, both in vivo and ex vivo. The term “innate immune response” includes a cellular response to exogenous nucleic acids, including single stranded nucleic acids, generally of viral or bacterial origin, which involves the induction of cytokine expression and release, particularly the interferons, and cell death. In some embodiments, the modified nucleosides, modified nucleotides, and modified nucleic acids described herein can disrupt binding of a major groove interacting partner with the nucleic acid.

In some embodiments, the modified nucleosides, modified nucleotides, and modified nucleic acids described herein can exhibit a reduced innate immune response when introduced into a population of cells, both in vivo and ex vivo, and also disrupt binding of a major groove interacting partner with the nucleic acid.

Definitions of Chemical Groups

As used herein, “alkyl” is meant to refer to a saturated hydrocarbon group which is straight-chained or branched. Example alkyl groups include methyl (Me), ethyl (Et), propyl (e.g., n-propyl and isopropyl), butyl (e.g., n-butyl, isobutyl, t-butyl), pentyl (e.g., n-pentyl, isopentyl, neopentyl), and the like. An alkyl group can contain from 1 to about 20, from 2 to about 20, from 1 to about 12, from 1 to about 8, from 1 to about 6, from 1 to about 4, or from 1 to about 3 carbon atoms.

As used herein, “aryl” refers to monocyclic or polycyclic (e.g., having 2, 3 or 4 fused rings) aromatic hydrocarbons such as, for example, phenyl, naphthyl, anthracenyl, phenanthrenyl, indanyl, indenyl, and the like. In some embodiments, aryl groups have from 6 to about 20 carbon atoms.

As used herein, “alkenyl” refers to an aliphatic group containing at least one double bond. As used herein, “alkynyl” refers to a straight or branched hydrocarbon chain containing 2-12 carbon atoms and characterized in having one or more triple bonds. Examples of alkynyl groups include, but are not limited to, ethynyl, propargyl, and 3-hexynyl.

As used herein, “arylalkyl” or “aralkyl” refers to an alkyl moiety in which an alkyl hydrogen atom is replaced by an aryl group. Aralkyl includes groups in which more than one hydrogen atom has been replaced by an aryl group. Examples of “arylalkyl” or “aralkyl” include benzyl, 2-phenylethyl, 3-phenylpropyl, 9-fluorenyl, benzhydryl, and trityl groups.

As used herein, “cycloalkyl” refers to a cyclic, bicyclic, tricyclic, or polycyclic non-aromatic hydrocarbon groups having 3 to 12 carbons. Examples of cycloalkyl moieties include, but are not limited to, cyclopropyl, cyclopentyl, and cyclohexyl.

As used herein, “heterocyclyl” refers to a monovalent radical of a heterocyclic ring system. Representative heterocyclyls include, without limitation, tetrahydrofuranyl, tetrahydrothienyl, pyrrolidinyl, pyrrolidonyl, piperidinyl, pyrrolinyl, piperazinyl, dioxanyl, dioxolanyl, diazepinyl, oxazepinyl, thiazepinyl, and morpholinyl.

As used herein, “heteroaryl” refers to a monovalent radical of a heteroaromatic ring system. Examples of heteroaryl moieties include, but are not limited to, imidazolyl, oxazolyl, thiazolyl, triazolyl, pyrrolyl, furanyl, indolyl, thiophenyl pyrazolyl, pyridinyl, pyrazinyl, pyridazinyl, pyrimidinyl, indolizinyl, purinyl, naphthyridinyl, quinolyl, and pteridinyl.

Phosphate Backbone Modifications The Phosphate Group

In some embodiments, the phosphate group of a modified nucleotide can be modified by replacing one or more of the oxygens with a different substituent. Further, the modified nucleotide, e.g., modified nucleotide present in a modified nucleic acid, can include the wholesale replacement of an unmodified phosphate moiety with a modified phosphate as described herein. In some embodiments, the modification of the phosphate backbone can include alterations that result in either an uncharged linker or a charged linker with unsymmetrical charge distribution.

Examples of modified phosphate groups include, phosphorothioate, phosphoroselenates, borano phosphates, borano phosphate esters, hydrogen phosphonates, phosphoroamidates, alkyl or aryl phosphonates and phosphotriesters. In some embodiments, one of the non-bridging phosphate oxygen atoms in the phosphate backbone moiety can be replaced by any of the following groups: sulfur (S), selenium (Se), BR₃ (wherein R can be, e.g., hydrogen, alkyl, or aryl), C (e.g., an alkyl group, an aryl group, and the like), H, NR₂ (wherein R can be, e.g., hydrogen, alkyl, or aryl), or OR (wherein R can be, e.g., alkyl or aryl). The phosphorous atom in an unmodified phosphate group is achiral. However, replacement of one of the non-bridging oxygens with one of the above atoms or groups of atoms can render the phosphorous atom chiral; that is to say that a phosphorous atom in a phosphate group modified in this way is a stereogenic center. The stereogenic phosphorous atom can possess either the “R” configuration (herein Rp) or the “S” configuration (herein Sp).

Phosphorodithioates have both non-bridging oxygens replaced by sulfur. The phosphorus center in the phosphorodithioates is achiral which precludes the formation of oligoribonucleotide diastereomers. In some embodiments, modifications to one or both non-bridging oxygens can also include the replacement of the non-bridging oxygens with a group independently selected from S, Se, B, C, H, N, and OR (R can be, e.g., alkyl or aryl).

The phosphate linker can also be modified by replacement of a bridging oxygen, (i.e., the oxygen that links the phosphate to the nucleoside), with nitrogen (bridged phosphoroamidates), sulfur (bridged phosphorothioates) and carbon (bridged methylenephosphonates). The replacement can occur at either linking oxygen or at both of the linking oxygens.

Replacement of the Phosphate Group

The phosphate group can be replaced by non-phosphorus containing connectors. In some embodiments, the charge phosphate group can be replaced by a neutral moiety.

Examples of moieties which can replace the phosphate group can include, without limitation, e.g., methyl phosphonate, hydroxylamino, siloxane, carbonate, carboxymethyl, carbamate, amide, thioether, ethylene oxide linker, sulfonate, sulfonamide, thioformacetal, formacetal, oxime, methyleneimino, methylenemethylimino, methylenehydrazo, methylenedimethylhydrazo and methyleneoxymethylimino.

Replacement of the Ribophosphate Backbone

Scaffolds that can mimic nucleic acids can also be constructed wherein the phosphate linker and ribose sugar are replaced by nuclease resistant nucleoside or nucleotide surrogates. In some embodiments, the nucleobases can be tethered by a surrogate backbone. Examples can include, without limitation, the morpholino, cyclobutyl, pyrrolidine and peptide nucleic acid (PNA) nucleoside surrogates.

Sugar Modifications

The modified nucleosides and modified nucleotides can include one or more modifications to the sugar group. For example, the 2′ hydroxyl group (OH) can be modified or replaced with a number of different “oxy” or “deoxy” substituents. In some embodiments, modifications to the 2′ hydroxyl group can enhance the stability of the nucleic acid since the hydroxyl can no longer be deprotonated to form a 2′-alkoxide ion. The 2′-alkoxide can catalyze degradation by intramolecular nucleophilic attack on the linker phosphorus atom.

Examples of “oxy”-2′ hydroxyl group modifications can include alkoxy or aryloxy (OR, wherein “R” can be, e.g., alkyl, cycloalkyl, aryl, aralkyl, heteroaryl or a sugar); polyethyleneglycols (PEG), 0(CH₂CH₂0)_(n)CH2CH₂OR wherein R can be, e.g., H or optionally substituted alkyl, and n can be an integer from 0 to 20 (e.g., from 0 to 4, from 0 to 8, from 0 to 10, from 0 to 16, from 1 to 4, from 1 to 8, from 1 to 10, from 1 to 16, from 1 to 20, from 2 to 4, from 2 to 8, from 2 to 10, from 2 to 16, from 2 to 20, from 4 to 8, from 4 to 10, from 4 to 16, and from 4 to 20). In some embodiments, the “oxy”-2′ hydroxyl group modification can include “locked” nucleic acids (LNA) in which the 2′ hydroxyl can be connected, e.g., by a Ci-₆ alkylene or Cj-6 heteroalkylene bridge, to the 4′ carbon of the same ribose sugar, where exemplary bridges can include methylene, propylene, ether, or amino bridges; O-amino (wherein amino can be, e.g., NH₂; alkylamino, dialkylamino, heterocyclyl, arylamino, diarylamino, heteroarylamino, or diheteroarylamino, ethylenediamine, or polyamino) and aminoalkoxy, 0(CH₂)_(n)-amino, (wherein amino can be, e.g., NH₂; alkylamino, dialkylamino, heterocyclyl, arylamino, diarylamino, heteroarylamino, or diheteroarylamino, ethylenediamine, or polyamino). In some embodiments, the “oxy”-2′ hydroxyl group modification can include the methoxyethyl group (MOE), (OCH₂CH₂OCH₃, e.g., a PEG derivative).

“Deoxy” modifications can include hydrogen (i.e. deoxyribose sugars, e.g., at the overhang portions of partially ds RNA); halo (e.g., bromo, chloro, fluoro, or iodo); amino (wherein amino can be, e.g., NH₂; alkylamino, dialkylamino, heterocyclyl, arylamino, diarylamino, heteroarylamino, diheteroarylamino, or amino acid); NH(CH₂CH₂NH)_(n)CH2CH₂— amino (wherein amino can be, e.g., as described herein), —NHC(0)R (wherein R can be, e.g., alkyl, cycloalkyl, aryl, aralkyl, heteroaryl or sugar), cyano; mercapto; alkyl-thio-alkyl; thioalkoxy; and alkyl, cycloalkyl, aryl, alkenyl and alkynyl, which may be optionally substituted with e.g., an amino as described herein.

The sugar group can also contain one or more carbons that possess the opposite stereochemical configuration than that of the corresponding carbon in ribose. Thus, a modified nucleic acid can include nucleotides containing e.g., arabinose, as the sugar. The nucleotide “monomer” can have an alpha linkage at the F position on the sugar, e.g., alpha-nucleosides. The modified nucleic acids can also include “abasic” sugars, which lack a nucleobase at C—. These abasic sugars can also be further modified at one or more of the constituent sugar atoms. The modified nucleic acids can also include one or more sugars that are in the L form, e.g. L-nucleosides.

Generally, RNA includes the sugar group ribose, which is a 5-membered ring having an oxygen. Exemplary modified nucleosides and modified nucleotides can include, without limitation, replacement of the oxygen in ribose (e.g., with sulfur (S), selenium (Se), or alkylene, such as, e.g., methylene or ethylene); addition of a double bond (e.g., to replace ribose with cyclopentenyl or cyclohexenyl); ring contraction of ribose (e.g., to form a 4-membered ring of cyclobutane or oxetane); ring expansion of ribose (e.g., to form a 6- or 7-membered ring having an additional carbon or heteroatom, such as for example, anhydrohexitol, altritol, mannitol, cyclohexanyl, cyclohexenyl, and morpholino that also has a phosphoramidate backbone). In some embodiments, the modified nucleotides can include multicyclic forms (e.g., tricyclo; and “unlocked” forms, such as glycol nucleic acid (GNA) (e.g., R-GNA or S-GNA, where ribose is replaced by glycol units attached to phosphodiester bonds), threose nucleic acid (TNA, where ribose is replaced with a-L-threofuranosyl-(3′-→2′)).

Modifications on the Nucleobase

The modified nucleosides and modified nucleotides described herein, which can be incorporated into a modified nucleic acid, can include a modified nucleobase. Examples of nucleobases include, but are not limited to, adenine (A), guanine (G), cytosine (C), and uracil (U). These nucleobases can be modified or wholly replaced to provide modified nucleosides and modified nucleotides that can be incorporated into modified nucleic acids. The nucleobase of the nucleotide can be independently selected from a purine, a pyrimidine, a purine or pyrimidine analog. In some embodiments, the nucleobase can include, for example, naturally-occurring and synthetic derivatives of a base.

Uracil

In some embodiments, the modified nucleobase is a modified uracil. Exemplary nucleobases and nucleosides having a modified uracil include without limitation pseudouridine (ψ), pyridin-4-one ribonucleoside, 5-aza-uridine, 6-aza-uridine, 2-thio-5-aza-uridine, 2-thio-uridine (s2U), 4-thio-uridine (s4U), 4-thio-pseudouridine, 2-thio-pseudouridine, 5-hydroxy-u,ridine (ho⁵U), 5-aminoallyl-uridine, 5-halo-uridine (e.g., 5-iodo-uridine or 5-bromo-uridine), 3-methyl-uridine (m³U), 5-methoxy-uridine (mo⁵U), uridine 5-oxyacetic acid (cmo⁵U), uridine 5-oxyacetic acid methyl ester (mcmôU), 5-carboxymethyl-uridine (cm^(s)U), 1-carboxymethyl-pseudouridine, 5-carboxyhydroxymethyl-uridine (chm⁵U), 5-carboxyhydroxymethyl-uridine methyl ester (mchm⁵U), 5-methoxycarbonylmethyl-uridine (mcm⁵U), 5-methoxycarbonylmethyl-2-thio-uridine (mcm⁵s2U), 5-aminomethyl-2-thio-uridine (nm⁵s2U), 5-methylaminomethyl-uridine (mnm⁵U), 5-methylaminomethyl-2-thio-uridine (mnm⁵s2U), 5-methylaminomethyl-2-seleno-uridine (mnm⁵se²U), 5-carbamoylmethyl-uridine (ncm⁵U), 5-carboxymethylaminomethyl-uridine (cmnm⁵U), 5-carboxymethylaminomethyl-2-thio-uridine (cmnm \s2U), 5-propynyl-uridine, 1-propynyl-pseudouridine, 5-taurinomethyl-uridine (xcm⁵U), 1-taurinomethyl-pseudouridine, 5-taurinomethyl-2-thio-uridine(Trn⁵s2U), 1-taurinomethyl-4-thio-pseudouridine, 5-methyl-uridine (m⁵U, i.e., having the nucleobase deoxythymine), 1-methyl-pseudouridine (ιτι′ψ). 5-methyl-2-thio-uridine (m⁵s2U), l-methyl-4-thio-pseudouridine (m's \|/), 4-thio-1-methyl-pseudouridine, 3-methyl-pseudouridine (m′V), 2-thio-1-methyl-pseudouridine, 1-methyl-1-deaza-pseudouridine, 2-thio-1-methyl-1-deaza-pseudouridine, dihydroundine (D), dihydropseudoundine, 5,6-dihydrouridine, 5-methyl-dihydrouridine (m⁵D), 2-thio-dihydrouridine, 2-thio-dihydropseudouridine, 2-methoxy-uridine, 2-methoxy-4-thio-uridine, 4-methoxy-pseudouridine, 4-methoxy-2-thio-pseudouridine, N1-methyl-pseudouridine, 3-(3-amino-3-carboxypropyl)uridine (acp³U), 1-methyl-3-(3-amino-3-carboxypropy pseudouridine 5-(isopentenylaminomethyl)uridine (inm⁵U), 5-(isopentenylaminomethyp-2-thio-uridine (inm⁵s2U), a-thio-uridine, 2′-0-methyl-uridine (Urn), 5,2′-0-dimethyl-uridine (m⁵Um), 2′-0-methyl-pseudouridine (ψπι), 2-thio-2′-0-methyl-uridine (s2Um), 5-methoxycarbonylmethyl-2′-0-methyl-uridine (mcm ⁵Um), 5-carbamoylmethyl-2′-0-methyl-uridine (ncm ⁵Um), 5-carboxymethylaminomethyl-2′-0-methyl-uridine (cmnm ⁵Um), 3,2′-0-dimethyl-uridine (m³Um), 5-(isopentenylaminomethyl)-2′-0-methyl-uridine (inm⁵Um), 1-thio-uridine, deoxythymidine, 2′-F-ara-uridine, 2′-F-uridine, 2′-OH-ara-uridine, 5-(2-carbomethoxyvinyl) uridine, 5-[3-(1-E-propenylamino)uridine, pyrazolo[3,4-d]pyrimidines, xanthine, and hypoxanthine.

Cytosine

In some embodiments, the modified nucleobase is a modified cytosine. Exemplary nucleobases and nucleosides having a modified cytosine include without limitation 5-aza-cytidine, 6-aza-cytidine, pseudoisocytidine, 3-methyl-cytidine (m³C), N4-acetyl-cytidine (act), 5-formyl-cytidine (f⁵C), N4-methyl-cytidine (m⁴C), 5-methyl-cytidine (m⁵C), 5-halo-cytidine (e.g., 5-iodo-cytidine), 5-hydroxymethyl-cytidine (hm⁵C), 1-methyl-pseudoisocytidine, pyrrolo-cytidine, pyrrolo-pseudoisocytidine, 2-thio-cytidine (s2C), 2-thio-5-methyl-cytidine, 4-thio-pseudoisocytidine, 4-thio-1-methyl-pseudoisocytidine, 4-thio-1-methyl-1-deaza-pseudoisocytidine, 1-methyl-1-deaza-pseudoisocytidine, zebularine, 5-aza-zebularine, 5-methyl-zebularine, 5-aza-2-thio-zebularine, 2-thio-zebularine, 2-methoxy-cytidine, 2-methoxy-5-methyl-cytidine, 4-methoxy-pseudoisocytidine, 4-methoxy-1-methyl-pseudoisocytidine, lysidine (k²C), a-thio-cytidine, 2′-0-methyl-cytidine (Cm), 5,2′-0-dimethyl-cytidine (m⁵Cm), N4-acetyl-2′-0-methyl-cytidine (ac⁴Cm), N4,2′-0-dimethyl-cytidine (m⁴Cm), 5-formyl-2′-0-methyl-cytidine (f ⁵Cm), N4,N4,2′-0-trimethyl-cytidine (m⁴ ₂Cm), 1-thio-cytidine, 2′-F-ara-cytidine, 2′-F-cytidine, and 2′-OH-ara-cytidine.

Adenine

In some embodiments, the modified nucleobase is a modified adenine. Exemplary nucleobases and nucleosides having a modified adenine include without limitation 2-amino-purine, 2,6-diaminopurine, 2-amino-6-halo-purine (e.g., 2-amino-6-chloro-purine), 6-halo-purine (e.g., 6-chloi-purine), 2-amino-6-methyl-purine, 8-azido-adenosine, 7-deaza-adenine, 7-deaza-8-aza-adenine, 7-deaza-2-amino-purine, 7-deaza-8-aza-2-amino-purine, 7-deaza-2,6-diaminopurine, 7-deaza-8-aza-2,6-diaminopurine, 1-methyl-adenosine (m′A), 2-methyl-adenine (m A), N6-methyl-adenosine (m⁶A), 2-methylthio-N6-methyl-adenosine (ms2 m⁶A), N6-isopentenyl-adenosine 2-methylthio-N6-isopentenyl-adenosine (ms²i⁶A), N6-(cis-hydroxyisopentenyl)adenosine (io⁶A), 2-methylthio-N6-(cis-hydroxyisopentenyl)adenosine (ms2io⁶A), N6-glycinylcarbamoyl-adenosine (g⁶A), N6-threonylcarbamoyl-adenosine (t⁶A), N6-methyl-N6-threonylcarbamoyl-adenosine (m⁶t⁶A), 2-methylthio-N6-threonylcarbamoyl-adenosine (ms²g⁶A), N6,N6-dimethyl-adenosine (m⁶ ₂A), N6-hydroxynorvalylcarbamoyl-adenosine (hn⁶A), 2-methylthio-N6-hydroxynorvalylcarbamoyl-adenosine (ms2hn⁶A), N6-acetyl-adenosine (ac⁶A), 7-methyl-adenine, 2-methylthio-adenine, 2-methoxy-adenine, a-thio-adenosine, 2′-0-methyl-adenosine (Am), N⁶,2′-0-dimethyl-adenosine (m⁵Am), N⁶-Methyl-2′-deoxyadenosine, N6,N6,2′-0-trimethyl-adenosine (m⁶ ₂Am), 1,2′-0-dimethyl-adenosine (m′ Am), 2′-0-ribosyladenosine (phosphate) (Ar(p)), 2-amino-N6-methyl-purine, 1-thio-adenosine, 8-azido-adenosine, 2′-F-ara-adenosine, 2′-F-adenosine, 2′-OH-ara-adenosine, and N6-(19-amino-pentaoxanonadecyl)-adenosine.

Guanine

In some embodiments, the modified nucleobase is a modified guanine. Exemplary nucleobases and nucleosides having a modified guanine include without limitation inosine (I), 1-methyl-inosine (m′l), wyosine (imG), methylwyosine (mimG), 4-demethyl-wyo″sine (imG-14), isowyosine (imG2), wybutosine (yW), peroxywybutosine (o₂yW), hydroxywybutosine (OHyW), undemriodified hydroxywybutosine (OHyW*), 7-deaza-guanosine, queuosine (Q), epoxyqueuosine (oQ), galactosyl-queuosine (galQ), mannosyl-queuosine (manQ), 7-cyano-7-deaza-guanosine (preQ₀), 7-aminomethyl-7-deaza-guanosine (preQi), archaeosine (G⁺), 7-deaza-8-aza-guanosine, 6-thio-guanosine, 6-thio-7-deaza-guanosine, 6-thio-7-deaza-8-aza-guanosine, 7-methyl-guanosine (m⁷G), 6-thio-7-methyl-guanosine, 7-methyl-inosine, 6-methoxy-guanosine, 1-methyl-guanosine (m′G), N2-methyl-guanosine (m²G), N2,N2-dimethyl-guanosine (m² ₂G), N2,7-dimethyl-guanosine (m²,7G), N2, N2,7-dimethyl-guanosine (m²,2,7G), 8-oxo-guanosine, 7-methyl-8-oxo-guanosine, 1-meth thio-guanosine, N2-methyl-6-thio-guanosine, N2,N2-dimethyl-6-thio-guanosine, a-thio-guanosine, 2′-0-methyl-guanosine (Gm), N2-methyl-2′-0-methyl-guanosine (m¾m), N2,N2-dimethyl-2′-0-methyl-guanosine (m² ₂Gm), 1-methyl-2′-0-methyl-guanosine (m′Gm), N2,7-dimethyl-2′-0-methyl-guanosine (m²,7Gm), 2′-0-methyl-inosine (Im), 1,2′-0-dimethyl-inosine (m′lm), 0⁶-phenyl-2′-deoxyinosine, 2′-0-ribosylguanosine (phosphate) (Gr(p)), 1-thio-guanosine, 0⁶-methy]-guanosine, 0⁶-Methyl-2′-deoxyguanosine, 2′-F-ara-guanosine, and 2′-F-guanosine.

Modified gRNAs

In some embodiments, the modified nucleic acids can be modified gRNAs. In some embodiments, gRNAs can be modified at the 3′ end. In this embodiment, the gRNAs can be modified at the 3′ terminal U ribose. For example, the two terminal hydroxyl groups of the U ribose can be oxidized to aldehyde groups and a concomitant opening of the ribose ring to afford a modified nucleoside, wherein U can be an unmodified or modified uridine.

In another embodiment, the 3′ terminal U can be modified with a 2′ 3′ cyclic phosphate, wherein U can be an unmodified or modified uridine. In some embodiments, the gRNA molecules may contain 3′ nucleotides which can be stabilized against degradation, e.g., by incorporating one or more of the modified nucleotides described herein. In this embodiment, e.g., uridines can be replaced with modified uridines, e.g., 5-(2-amino)propyl uridine, and 5-bromo uridine, or with any of the modified uridines described herein; adenosines and guanosines can be replaced with modified adenosines and guanosines, e.g., with modifications at the 8-position, e.g., 8-bromo guanosine, or with any of the modified adenosines or guanosines described herein. In some embodiments, deaza nucleotides, e.g., 7-deaza-adenosine, can be incorporated into the gRNA. In some embodiments, O- and N-alkylated nucleotides, e.g., N6-methyl andenosine, can be incorporated into the gRNA. In some embodiments, sugar-modified ribonucleotides can be incorporated, e.g., wherein the 2′ OH— group is replaced by a group selected from H, —OR, —R (wherein R can be, e.g., methyl, alkyl, cycloalkyl, aryl, aralkyl, heteroaryl or sugar), halo, —SH, —SR (wherein R can be, e.g., alkyl, cycloalkyl, aryl, aralkyl, heteroaryl or sugar), amino (wherein amino can be, e.g., NH₂; alkylamino, dialkylamino, heterocyclyl, arylamino, diarylamino, heteroarylamino, diheteroarylamino, or amino acid); or cyano (—CN). In some embodiments, the phosphate backbone can be modified as described herein, e.g., with a phosphothioate group. In some embodiments, the nucleotides in the overhang region of the gRNA can each independently be a modified or unmodified nucleotide including, but not limited to 2′-sugar modified, such as, 2-F 2′-0-methyl, thymidine (T), 2′-O-methoxyethyl-5-methyluridine (Teo), 2′-O-methoxyethyladenosine (Aeo), 2′-O-methoxyethyl-5-methylcytidine (m5Ceo), and any combinations thereof.

In an embodiment, a one or more or all of the nucleotides in single stranded overhang of an RNA molecule, e.g., a gRNA molecule, are deoxynucleotides.

Pharmaceutical Compositions

Pharmaceutical compositions of the present invention may comprise a gRNA molecule described herein, e.g., a plurality of gRNA molecules as described herein, or a cell (e.g., a population of cells, e.g., a population of hematopoietic stem cells, e.g., of CD34+ cells) comprising one or more cells modified with one or more gRNA molecules described herein, in combination with one or more pharmaceutically or physiologically acceptable carriers, diluents or excipients. Such compositions may comprise buffers such as neutral buffered saline, phosphate buffered saline and the like; carbohydrates such as glucose, mannose, sucrose or dextrans, mannitol; proteins; polypeptides or amino acids such as glycine; antioxidants; chelating agents such as EDTA or glutathione; adjuvants (e.g., aluminum hydroxide); and preservatives. Compositions of the present invention are in one aspect formulated for intravenous administration.

Pharmaceutical compositions of the present invention may be administered in a manner appropriate to the disease to be treated (or prevented). The quantity and frequency of administration will be determined by such factors as the condition of the patient, and the type and severity of the patient's disease, although appropriate dosages may be determined by clinical trials.

In one embodiment, the pharmaceutical composition is substantially free of, e.g., there are no detectable levels of a contaminant, e.g., selected from the group consisting of endotoxin, mycoplasma, mouse antibodies, pooled human serum, bovine serum albumin, bovine serum, culture media components, unwanted CRISPR system components, a bacterium and a fungus. In one embodiment, the bacterium is at least one selected from the group consisting of Alcaligenes faecalis, Candida albicans, Escherichia coli, Haemophilus influenza, Neisseria meningitides, Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus pneumonia, and Streptococcus pyogenes group A.

The administration of the subject compositions may be carried out in any convenient manner, including by aerosol inhalation, injection, ingestion, transfusion, implantation or transplantation. The compositions described herein may be administered to a patient transarterially, subcutaneously, intradermally, intratumorally, intranodally, intramedullary, intramuscularly, by intravenous (i.v.) injection, or intraperitoneally. In one aspect, the compositions of the present invention are administered to a patient by intradermal or subcutaneous injection. In one aspect, the cell compositions of the present invention are administered by i.v. injection.

The dosage of the above treatments to be administered to a patient will vary with the precise nature of the condition being treated and the recipient of the treatment. The scaling of dosages for human administration can be performed according to art-accepted practices.

Cells

The invention also relates to cells comprising a gRNA molecule of the invention, or nucleic acid encoding said gRNA molecules.

In an aspect the cells are cells made by a process described herein.

In embodiments, the cells are hematopoietic stem cells (e.g., hematopoietic stem and progenitor cells; HSPCs), for example, CD34+ stem cells. In embodiments, the cells are CD34+/CD90+ stem cells. In embodiments, the cells are CD34+/CD90− stem cells. In embodiments, the cells are human hematopoietic stem cells. In embodiments, the cells are autologous. In embodiments, the cells are allogeneic.

In embodiments, the cells are derived from bone marrow, e.g., autologous bone marrow. In embodiments, the cells are derived from peripheral blood, e.g., mobilized peripheral blood, e.g., autologous mobilized peripheral blood. In embodiments employing moblized peripheral blood, the cells are isoalted from patients who have been administered a mobilization agent. In embodiments, the mobilization agent is G-CSF. In embodiments, the mobilization agent is Plerixafor® (AMD3100). In embodiments, the cells are derived from umbilical cord blood, e.g., allogeneic umbilical cord blood.

In embodiments, the cells are mammalian. In embodiments, the cells are human.

In an aspect, the invention provides a cell comprising a modification or alteration, e.g., an indel, at or near (e.g., within 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1 nucleotides of) a nucleic acid sequence having complementarity to a gRNA molecule or gRNA molecules, e.g., as described herein, introduced into said cells, e.g., as part of a CRISPR system as described herein. In embodiments, the cell is a CD34+ cell. In embodiments, the altered or modified cell, e.g., CD34+ cell, maintains the ability to differentiate into cells of multiple lineages, e.g., maintains the ability to differentiate into cells of the erythroid lineage. In embodiments, the altered or modified cell, e.g., CD34+ cell, has undergone or is able to undergo at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9 or at least 10 or more doublings in culture, e.g., in culture comprising a stem cell expander, e.g., Compound 4. In embodiments, the altered or modified cell, e.g., CD34+ cell, has undergone or is able to undergo at least 5, e.g., about 5, doublings in culture, e.g., in culture comprising a stem cell expander molecule, e.g., as described herein, e.g., Compound 4. In embodiments the altered or modified cell, e.g., CD34+ cell, exhibits and/or is able to differentiate into a cell, e.g., into a cell of the erythroid lineage, e.g., into a red blood cell, that exhibits increased fetal hemoglobin level (e.g., expression level and/or protein level), e.g., at least a 20% increase in fetal hemoglobin protein level, relative to a similar unmodified or unaltered cell. In embodiments the altered or modified cell, e.g., CD34+ cell, exhibits and/or is able to differentiate into a cell, e.g., into a cell of the erythroid lineage, e.g., into a red blood cell, that exhibits increased fetal hemoglobin level (e.g., expression level and/or protein level), relative to a similar unmodified or unaltered cell, e.g., produces at least 6 picograms, e.g., at least 7 picograms, at least 8 picograms, at least 9 picograms, or at least 10 picograms of fetal hemoglobin. In embodiments the altered or modified cell, e.g., CD34+ cell, exhibits and/or is able to differentiate into a cell, e.g., into a cell of the erythroid lineage, e.g., into a red blood cell, that exhibits increased fetal hemoglobin level (e.g., expression level and/or protein level), relative to a similar unmodified or unaltered cell, e.g., produces about 6 to about 12, about about 6 to about 7, about 7 to about 8, about 8 to about 9, about 9 to about 10, about 10 to about 11 or about 11 to about 12 picograms of fetal hemoglobin.

In an aspect, the invention provides a population of cells comprising cells having a modification or alteration, e.g., an indel, at or near (e.g., within 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1 nucleotides of) a nucleic acid sequence having complementarity to a gRNA molecule or gRNA molecules, e.g., as described herein, introduced into said cells, e.g., as part of a CRISPR system as described herein. In embodiments, at least 50%, e.g., at least 60%, at least 70%, at least 80% or at least 90% of the cells of the population have the modification or alteration (e.g., have at least one modification or alteration), e.g., as measured by NGS, e.g., as described herein, e.g., at day two following introduction of the gRNA and/or CRISPR system of the invention. In embodiments, at least 90%, e.g., at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% of the cells of the population have the modification or alteration (e.g., have at least one modification or alteration), e.g., as measured by NGS, e.g., as described herein, e.g., at day two following introduction of the gRNA and/or CRISPR system of the invention. In embodiments, the population of cells comprise CD34+ cells, e.g., comprise at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95% or at least about 98% CD34+ cells. In embodiments, the population of cells comprising the altered or modified cells, e.g., CD34+ cells, maintain the ability to produce, e.g., differentiate into, cells of multiple lineages, e.g., maintains the ability to produce, e.g., differentiate into, cells of the erythroid lineage. In embodiments, the population of cells, e.g., population of CD34+ cells, has undergone or is able to undergo at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9 or at least 10 or more population doublings in culture, e.g., in culture comprising a stem cell expander, e.g., Compound 4. In embodiments, the population of altered or modified cells, e.g., population of CD34+ cells, has undergone or is capable of undergoing at least 5, e.g., about 5, population doublings in culture, e.g., in culture comprising a stem cell expander molecule, e.g., as described herein, e.g., Compound 4. In embodiments the population of cells comprising altered or modified cells, e.g., CD34+ cells, exhibits and/or is able to differentiate into a population of cells, e.g., into a population of cells of the erythroid lineage, e.g., into a population of red blood cells, that exhibits increased fetal hemoglobin level (e.g., expression level and/or protein level), e.g., at least a 20% increase in fetal hemoglobin protein level, relative to a similar unmodified or unaltered cells. In embodiments the population of cells comprising altered or modified cells, e.g., CD34+ cells, exhibits and/or is able to differentiate into a population of cells, e.g., into a population of cells of the erythroid lineage, e.g., into a population of red blood cells, that exhibits increased fetal hemoglobin level (e.g., expression level and/or protein level), relative to a similar unmodified or unaltered cells, e.g., comprises cells that produce at least 6 picograms, e.g., at least 7 picograms, at least 8 picograms, at least 9 picograms, or at least 10 picograms of fetal hemoglobin per cell. In embodiments the population of altered or modified cells, e.g., CD34+ cells, exhibits and/or is able to differentiate into a population of cells, e.g., into a population of cells of the erythroid lineage, e.g., into a population of red blood cells, that exhibits increased fetal hemoglobin level (e.g., expression level and/or protein level), relative to a similar unmodified or unaltered cell, e.g., comprises cells that produce about 6 to about 12, about about 6 to about 7, about 7 to about 8, about 8 to about 9, about 9 to about 10, about 10 to about 11 or about 11 to about 12 picograms of fetal hemoglobin per cell.

In embodiments, the population of cells, e.g., as described herein, comprises at least about 1e3 cells.

In embodiments, the population of cells, e.g., as described herein, comprises at least about 1e4 cells.

In embodiments, the population of cells, e.g., as described herein, comprises at least about 1e5 cells.

In embodiments, the population of cells, e.g., as described herein, comprises at least about 1e6 cells.

In embodiments, the population of cells, e.g., as described herein, comprises at least about 1e7 cells.

In embodiments, the population of cells, e.g., as described herein, comprises at least about 1e8 cells.

In embodiments, the population of cells, e.g., as described herein, comprises at least about 1e9 cells.

In embodiments, the population of cells, e.g., as described herein, comprises at least about 1e10 cells.

In embodiments, the population of cells, e.g., as described herein, comprises at least about 1e11 cells.

In embodiments, the population of cells, e.g., as described herein, comprises at least about 1e12 cells.

In embodiments, the population of cells, e.g., as described herein, comprises at least about 1e13 cells per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 1e6 cells per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 2e6 cells per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 3e6 cells per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 4e6 cells per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 5e6 cells per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 6e6 cells per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 7e6 cells per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 8e6 cells per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 9e6 cells per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 1e7 cells per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 2e7 cells per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 3e7 cells per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 4e7 cells per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 5e7 cells per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 6e7 cells per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 7e7 cells per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 8e7 cells per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 9e7 cells per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 1e8 cells per kilogram body weight of the patient to which they are to be administered. In any of the aforementioned embodiments, the population of cells may comprise at least about 50% (for example, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95% or at least about 99%) HSPCs, e.g., CD34+ cells. In any of the aforementioned embodiments, the population of cells may comprise about 60% HSPCs, e.g., CD34+ cells. In an embodiment, the population of cells, e.g., as described herein, comprises about 3e7 cells and comprises about 2e7 HSPCs, e.g., CD34+ cells.

In embodiments, the population of cells, e.g., as described herein, comprises at least about 1e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 1.5e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 2e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 3e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 4e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 5e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 6e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 7e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 8e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 9e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 1e7 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 2e7 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 3e7 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 4e7 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 5e7 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 6e7 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 7e7 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 8e7 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 9e7 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 1e8 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 2e8 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 3e8 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 4e8 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises at least about 5e8 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered.

In embodiments, the population of cells, e.g., as described herein, comprises about 1e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 1.5e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 2e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 3e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 4e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 5e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 6e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 7e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 8e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 9e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 1e7 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 2e7 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 3e7 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 4e7 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 5e7 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 6e7 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 7e7 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 8e7 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 9e7 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 1e8 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 2e8 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 3e8 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 4e8 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises about 5e8 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered.

In embodiments, the population of cells, e.g., as described herein, comprises from about 2e6 to about 10e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered. In embodiments, the population of cells, e.g., as described herein, comprises from 2e6 to 10e6 HSPCs, e.g., CD34+ cells, per kilogram body weight of the patient to which they are to be administered.

The cells of the invention may comprise a gRNA molecule of the present invention, or nucleic acid encoding said gRNA molecule, and a Cas9 molecule of the present invention, or nucleic acid encoding said Cas9 molecule. In an embodiment, the cells of the invention may comprise a ribonuclear protein (RNP) complex which comprises a gRNA molecule of the invention and a Cas9 molecule of the invention.

The cells of the invention are preferrably modified to comprise a gRNA molecule of the invention ex vivo, for example by a method described herein, e.g., by electroporation.

The cells of the invention include cells in which expression of one or more genes has been altered, for example, reduced or inhibited, by introduction of a CRISPR system comprising a gRNA of the invention. For example, the cells of the present invention may have a reduced level of BCL11a expression relative to unmodified cells. As another example, the cells of the present invention may have an increased level of fetal hemoglobin expression relative to unmodified cells. As another example, the cells of the present invention may have reduced level of beta globin expression relative to unmodified cells. Alternatively, or in addition, a cell of the invention may give rise, e.g., differentiate into, another type of cell, e.g., an erythrocyte, that has a reduced level of BCL11a expression relative to cells differentiated from unmodified cells. Alternatively, or in addition, a cell of the invention may give rise, e.g., differentiate into, another type of cell, e.g., an erythrocyte, that has an increased level of fetal hemoglobin expression relative to cells differentiated from unmodified cells. Alternatively, or in addition, a cell of the invention may give rise, e.g., differentiate into, another type of cell, e.g., an erythrocyte, that has a reduced level of beta globin expression relative to cells differentiated from unmodified cells.

The cells of the invention include cells in which expression of one or more genes has been altered, for example, reduced or inhibited, by introduction of a CRISPR system comprising a gRNA of the invention. For example, the cells of the present invention may have a reduced level of hemeoglobin beta, for example a mutated or wild-type hemoglobin beta, expression relative to unmodified cells. In another aspect, the invention provides cells which are derived from, e.g., differentiated from, cells in which a CRISPR system comprising a gRNA of the invention has been introduced. In such aspects, the cells in which the CRISPR system comprising the gRNA of the invention has been introduced may not exhibit the reduced level of hemoglobin beta, for example a mutated or wild-type hemoglobin beta, but the cells derived from, e.g., differentiated from, said cells exhibit the reduced level of hemoglobin beta, for example a mutated or wild-type hemoglobin beta. In embodiments, the derivation, e.g., differentiation, is accomplished in vivo (e.g., in a patient). In embodiments the cells in which the CRISPR system comprising the gRNA of the invention has been introduced are CD34+ cells and the cells derived, e.g., differentiated, therefrom are of the erythroid lineage, e.g., red blood cells.

The cells of the invention include cells in which expression of one or more genes has been altered, for example, increased or promoted, by introduction of a CRISPR system comprising a gRNA of the invention. For example, the cells of the present invention may have an increased level of fetal hemoglobin expression relative to unmodified cells. In another aspect, the invention provides cells which are derived from, e.g., differentiated from, cells in which a CRISPR system comprising a gRNA of the invention has been introduced. In such aspects, the cells in which the CRISPR system comprising the gRNA of the invention has been introduced may not exhibit the increased level of fetal hemoglobin but the cells derived from, e.g., differentiated from, said cells exhibit the increased level of fetal hemoglobin. In embodiments, the derivation, e.g., differentiation, is accomplished in vivo (e.g., in a patient). In embodiments the cells in which the CRISPR system comprising the gRNA of the invention has been introduced are CD34+ cells and the cells derived, e.g., differentiated, therefrom are of the erythroid lineage, e.g., red blood cells.

In another aspect, the invention relates to cells which include an indel at (e.g., within) or near (e.g., within 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1 nucleotides of) a nucleic acid sequence having complementarity to the gRNA molecule or gRNA molecules introduced into said cells. In embodiments, the indel is a frameshift indel. In embodiments, the indel is an indel listed in Table 15. In embodiments, the indel is an indel listed in Table 26, Table 27 or Table 37. In embodiments the invention pertains to a population of cells, e.g., as described herein, wherein the population of cells comprises cells having an indel listed in Table 15. In embodiments the invention pertains to a population of cells, e.g., as described herein, wherein the population of cells comprises cells having an indel listed in Table 26, Table 27 or Table 37.

In an aspect, the invention relates to a population of cells, e.g., a population of HSPCs, which comprises cells which include an indel, e.g., as described herein, e.g., an indel or pattern of indels described in FIG. 25, Table 15, Table 26, Table 27 or Table 37, at or near (e.g., within 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1 nucleotides of) a nucleic acid sequence having complementarity to a gRNA molecule or gRNA molecules, e.g., as described herein, introduced into said cells, e.g., as described herein. In embodiments, the indel is a frameshift indel. In embodiments, 20%-100% of the cells of the population include said indel or indels. In embodiments, 30%-100% of the cells of the population include said indel or indels. In embodiments, 40%-100% of the cells of the population include said indel or indels. In embodiments, 50%-100% of the cells of the population include said indel or indels. In embodiments, 60%-100% of the cells of the population include said indel or indels. In embodiments, 70%-100% of the cells of the population include said indel or indels. In embodiments, 80%-100% of the cells of the population include said indel or indels. In embodiments, 90%-100% of the cells of the population include said indel or indels. In embodiments, the population of cells retains the ability to differentiate into multiple cell types, e.g., maintains the ability to differentiate into cells of erythroid lineage, e.g., red blood cells. In embodiments, the edited and differentiated cells (e.g., red blood cells) maintain the ability to proliferate, e.g., proliferate at least 5-fold, at least 10-fold, at least 15-fold, at least 20-fold, at least 25-fold, at least 30-fold, at least 35-fold, at least 40-fold, at least 45-fold, at least 50-fold or more after 7 days in erythroid differentiation medium (EDM), e.g., as described in the Examples, and/or, proliferate at least 30-fold, at least 35-fold, at least 40-fold, at least 45-fold, at least 50-fold, at least 55-fold, at least 60-fold, at least 65-fold, at least 70-fold, at least 75-fold, at least 80-fold, at least 85-fold, at least 90-fold, at least 95-fold, at least 100-fold, at least 110-fold, at least 120-fold, at least 130-fold, at least 140-fold, at least 150-fold, at least 200-fold, at least 300-fold, at least 400-fold, at least 500-fold, at least 600-fold, at least 700-fold, at least 800-fold, at least 900-fold, at least 1000-fold, at least 1100-fold, at least 1200-fold, at least 1300-fold, at least 1400-fold, at least 1500-fold or more after 21 days in erythroid differentiation medium (EDM), e.g., as described in the Examples,

In an embodiment, the invention provides a population of cells, e.g., CD34+ cells, of which at least 90%, e.g., at least 95%, e.g., at least 98%, of the cells of the population comprise an indel, e.g., as described herein (without being bound by theory, it is believed that introduction of a gRNA molecule or CRISPR system as described herein into a population of cells produces a pattern of indels in said population, and thus, each cell of the population which comprises an indel may not exhibit the same indel), at or near a site complementary to the targeting domain of a gRNA molecule described herein; wherein said cells maintain the ability to differentiate into cells of an erythroid lineage, e.g., red blood cells; and/or wherein said cells differentiated from the population of cells have an increased level of fetal hemoglobin (e.g., the population has a higher % F cells) relative to cells differentiated from a similar population of unmodified cells. In embodiments, the population of cells has undergone at least a 5-fold expansion ex vivo, e.g., in the media comprising Compound 4.

In embodiments, the indel is less than about 50 nucleotides, e.g., less than about 45, less than about 40, less than about 35, less than about 30 or less than about 25 nucleotides. In embodiments, the indel is less than about 25 nucleotides. In embodiments, the indel is less than about 20 nucleotides. In embodiments, the indel is less than about 15 nucleotides. In embodiments, the indel is less than about 10 nucleotides. In embodiments, the indel is less than about 9 nucleotides. In embodiments, the indel is less than about 9 nucleotides. In embodiments, the indel is less than about 7 nucleotides. In embodiments, the indel is less than about 6 nucleotides. In embodiments, the indel is less than about 5 nucleotides. In embodiments, the indel is less than about 4 nucleotides. In embodiments, the indel is less than about 3 nucleotides. In embodiments, the indel is less than about 2 nucleotides. In any of the aforementioned embodiments, the indel is at least 1 nucleotide. In embodiments, the indel is 1 nucleotide.

In an aspect, the invention provides a population of modified HSPCs or erythroid cells differentiated from said HSPCs (e.g., differentiated ex vivo or in a patient), e.g., as described herein, wherein at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% of the cells are F cells. In embodiments, the population of cells contains (or is capable of differentiating, e.g., in vivo, into a population of erythrocytes that contains) a higher percent of F cells than a similar population of cells which have not had a gRNA molecule or gRNA molecules, e.g., as described herein, introduced into said cells. In embodiments, the population of cells has (or is capable of differentiating, e.g., in vivo, into a population of erythrocytes that has) at least a 20% increase, e.g, at least 21% increase, at least 22% increase, at least 23% increase, at least 24% increase, at least 25% increase, at least 26% increase, at least 27% increase, at least 28% increase, or at least 29% increase, in F cells relative to the similar population of cells which have not had a gRNA molecule or gRNA molecules, e.g., as described herein, introduced into said cells. In embodiments, the population of cells has (or is capable of differentiating, e.g., in vivo, into a population of erythrocytes that has) at least a 30% increase, e.g., at least a 35% increase, at least a 40% increase, at least a 45% increase, at least a 50% increase, at least a 55% increase, at least a 60% increase, at least a 65% increase, at least a 70% increase, at least a 75% increase, at least a 80% increase, at least a 85% increase, at least a 90% increase or at least a 95% increase, in F cells relative to the similar population of cells which have not had a gRNA molecule or gRNA molecules, e.g., as described herein, introduced into said cells. In embodiments, the population of cells has (or is capable of differentiating, e.g., in vivo, into a population of erythrocytes that has) at a 10-90%, a 20%-80%, a 20%-70%, a 20%-60%, a 20%-50%, a 20%-40%, a 20%-30%, a 25%-80%, a 25%-70%, a 25%-60%, a 25%-50%, a 25%-40%, a 25%-35%, a 25%-30%, a 30%-80%, a 30%-70%, a 30%-60%, a 30%-50%, a 30%-40%, or a 30%-35% increase in F cells relative to the similar population of cells which have not had a gRNA molecule or gRNA molecules, e.g., as described herein, introduced into said cells. In embodiments, the population of cells, e.g., as produced by a method described herein, comprises a sufficient number or cells and/or a sufficient increase in % F cells to treat a hemoglobinopathy, e.g., as described herein, e.g., sickle cell disease and/or beta thalassemia, in a patient in need thereof when introduced into said patient, e.g., in a therapeutically effective amount. In embodiments, the increase in F cells is as measured in an erythroid differentiation assay, e.g., as described herein.

In embodiments, including in any of the embodiments and aspects described herein, the invention relates to a cell, e.g., a population of cells, e.g., as modified by any of the gRNA, methods and/or CRISPR systems described herein, comprising F cells that produce at least 6 picograms fetal hemoglobin per cell. In embodiments, the F cells produce at least 7 picograms fetal hemoglobin per cell. In embodiments, the F cells produce at least 8 picograms fetal hemoglobin per cell. In embodiments, the F cells produce at least 9 picograms fetal hemoglobin per cell. In embodiments, the F cells produce at least 10 picograms fetal hemoglobin per cell. In embodiments, the F cells produce an average of between 6.0 and 7.0 picograms, between 7.0 and 8.0, between 8.0 and 9.0, between 9.0 and 10.0, between 10.0 and 11.0, or between 11.0 and 12.0 picograms of fetal hemoglobin per cell.

In embodiments, including in any of the aforementioned embodiments, the cell and/or population of cells of the invention includes, e.g., consists of, cells which do not comprise nucleic acid encoding a Cas9 molecule.

Methods of Treatment Delivery Timing

In an embodiment, one or more nucleic acid molecules (e.g., DNA molecules) other than the components of a Cas system, e.g., the Cas9 molecule component and/or the gRNA molecule component described herein, are delivered. In an embodiment, the nucleic acid molecule is delivered at the same time as one or more of the components of the Cas system are delivered. In an embodiment, the nucleic acid molecule is delivered before or after (e.g., less than about 30 minutes, 1 hour, 2 hours, 3 hours, 6 hours, 9 hours, 12 hours, 1 day, 2 days, 3 days, 1 week, 2 weeks, or 4 weeks) one or more of the components of the Cas system are delivered. In an embodiment, the nucleic acid molecule is delivered by a different means than one or more of the components of the Cas system, e.g., the Cas9 molecule component and/or the gRNA molecule component, are delivered. The nucleic acid molecule can be delivered by any of the delivery methods described herein. For example, the nucleic acid molecule can be delivered by a viral vector, e.g., an integration-deficient lentivirus, and the Cas9 molecule component and/or the gRNA molecule component can be delivered by electroporation, e.g., such that the toxicity caused by nucleic acids (e.g., DNAs) can be reduced. In an embodiment, the nucleic acid molecule encodes a therapeutic protein, e.g., a protein described herein. In an embodiment, the nucleic acid molecule encodes an RNA molecule, e.g, an RNA molecule described herein.

Bi-Modal or Differential Delivery of Components

Separate delivery of the components of a Cas system, e.g., the Cas9 molecule component and the gRNA molecule component, and more particularly, delivery of the components by differing modes, can enhance performance, e.g., by improving tissue specificity and safety. In an embodiment, the Cas9 molecule and the gRNA molecule are delivered by different modes, or as sometimes referred to herein as differential modes. Different or differential modes, as used herein, refer modes of delivery, that confer different pharmacodynamic or pharmacokinetic properties on the subject component molecule, e.g., a Cas9 molecule, gRNA molecule, template nucleic acid, or payload. E.g., the modes of delivery can result in different tissue distribution, different half-life, or different temporal distribution, e.g., in a selected compartment, tissue, or organ.

Some modes of delivery, e.g., delivery by a nucleic acid vector that persists in a cell, or in progeny of a cell, e.g., by autonomous replication or insertion into cellular nucleic acid, result in more persistent expression of and presence of a component. Examples include viral, e.g., adeno associated virus or lentivirus, delivery.

By way of example, the components, e.g., a Cas9 molecule and a gRNA molecule, can be delivered by modes that differ in terms of resulting half life or persistent of the delivered component the body, or in a particular compartment, tissue or organ. In an embodiment, a gRNA molecule can be delivered by such modes. The Cas9 molecule component can be delivered by a mode which results in less persistence or less exposure of its to the body or a particular compartment or tissue or organ.

More generally, in an embodiment, a first mode of delivery is used to deliver a first component and a second mode of delivery is used to deliver a second component. The first mode of delivery confers a first pharmacodynamic or pharmacokinetic property. The first pharmacodynamic property can be, e.g., distribution, persistence, or exposure, of the component, or of a nucleic acid that encodes the component, in the body, a compartment, tissue or organ. The second mode of delivery confers a second pharmacodynamic or pharmacokinetic property. The second pharmacodynamic property can be, e.g., distribution, persistence, or exposure, of the component, or of a nucleic acid that encodes the component, in the body, a compartment, tissue or organ.

In an embodiment, the first pharmacodynamic or pharmacokinetic property, e.g., distribution, persistence or exposure, is more limited than the second pharmacodynamic or pharmacokinetic property.

In an embodiment, the first mode of delivery is selected to optimize, e.g., minimize, a pharmacodynamic or pharmacokinetic property, e.g., distribution, persistence or exposure.

In an embodiment, the second mode of delivery is selected to optimize, e.g., maximize, a pharmacodynamic or pharmcokinetic property, e.g., distribution, persistence or exposure.

In an embodiment, the first mode of delivery comprises the use of a relatively persistent element, e.g., a nucleic acid, e.g., a plasmid or viral vector, e.g., an AAV or lentivirus. As such vectors are relatively persistent product transcribed from them would be relatively persistent.

In an embodiment, the second mode of delivery comprises a relatively transient element, e.g., an RNA or protein.

In an embodiment, the first component comprises gRNA, and the delivery mode is relatively persistent, e.g., the gRNA is transcribed from a plasmid or viral vector, e.g., an AAV or lentivirus. Transcription of these genes would be of little physiological consequence because the genes do not encode for a protein product, and the gR As are incapable of acting in isolation. The second component, a Cas9 molecule, is delivered in a transient manner, for example as mRNA or as protein, ensuring that the full Cas9 molecule/gRNA molecule complex is only present and active for a short period of time.

Furthermore, the components can be delivered in different molecular form or with different delivery vectors that complement one another to enhance safety and tissue specificity.

Use of differential delivery modes can enhance performance,’ safety and efficacy. For example, the likelihood of an eventual off-target modification can be reduced. Delivery of immunogenic components, e.g., Cas9 molecules, by less persistent modes can reduce immunogenicity, as peptides from the bacterially-derived Cas enzyme are displayed on the surface of the cell by MHC molecules. A two-part delivery system can alleviate these drawbacks.

Differential delivery modes can be used to deliver components to different, but overlapping target regions. The formation active complex is minimized outside the overlap of the target regions. Thus, in an embodiment, a first component, e.g., a gRNA molecule is delivered by a first delivery mode that results in a first spatial, e.g., tissue, distribution. A second component, e.g., a Cas9 molecule is delivered by a second delivery mode that results in a second spatial, e.g., tissue, distribution. In an embodiment, the first mode comprises a first element selected from a liposome, nanoparticle, e.g., polymeric nanoparticle, and a nucleic acid, e.g., viral vector. The second mode comprises a second element selected from the group. In an embodiment, the first mode of delivery comprises a first targeting element, e.g., a cell specific receptor or an antibody, and the second mode of delivery does not include that element. In an embodiment, the second mode of delivery comprises a second targeting element, e.g., a second cell specific receptor or second antibody.

When the Cas9 molecule is delivered in a virus delivery vector, a liposome, or polymeric nanoparticle, there is the potential for delivery to and therapeutic activity in multiple tissues, when it may be desirable to only target a single tissue. A two-part delivery system can resolve this challenge and enhance tissue specificity. If the gRNA molecule and the Cas9 molecule are packaged in separated delivery vehicles with distinct but overlapping tissue tropism, the fully functional complex is only be formed in the tissue that is targeted by both vectors.

Candidate Cas molecules, e.g., Cas9 molecules, candidate gRNA molecules, candidate Cas9 molecule/gRNA molecule complexes, and candidate CRISPR systems, can be evaluated by art-known methods or as described herein. For example, exemplary methods for evaluating the endonuclease activity of Cas9 molecule are described, e.g., in Jinek el al., SCIENCE 2012; 337(6096):816-821.

EXAMPLES Example 1 Guide Selection and Design

Initial guide selection was performed in silico using a human reference genome and user defined genomic regions of interest (e.g., a gene, an exon of a gene, non-coding regulatory region, etc), for identifying PAMs in the regions of interest. For each identified PAM, analyses were performed and statistics reported. gRNA molecules were further selected and rank-ordered based on a number of methods for determining efficiency and efficacy, e.g., as described herein.

Throughout the Examples, in the experiments below, either sgRNA molecules or dgRNA molecules were used. Unless indicated otherwise, where dgRNA molecules were used, the gRNA includes the following:

crRNA: [targeting domain]-[SEQ ID NO: 6607] tracr (trRNA): SEQ ID NO: 6660

Unless indicated otherwise, in experiments employing a sgRNA molecule, the following sequence was used:

[targeting domain]-[SEQ ID NO: 6601]-UUUU

Unless indicated otherwise, in experiments employing a sgRNA molecule labeled “BC”, the following sequence was used:

[targeting domain]-[SEQ ID NO: 6604]-UUUU

Transfection of HEK-293 Cas9GFP Cells for Primary Guide Screening

Transfection of Cas9GFP-expressing HEK293 cells (HEK-293_Cas9GFP) was used for primary screening of target specific crRNAs. In this example, target specific crRNAs were designed and selected for primary screening using defined criteria including in silico off-target detection, e.g., as described herein. Selected crRNAs were chemically synthesized and delivered in a 96 well format. HEK-293-Cas9GFP cells were transfected with target crRNAs in a 1:1 ratio with stock trRNA. The transfection was mediated using lipofection technology according to manufacturer's protocol (Lipofectamine 2000, Life Technologies). Transfected cells were lysed 24 h following lipofection and editing (e.g., cleavage) was detected within lysates with the T7E1 assay and/or next generation sequencing (NGS; below).

T7E1 Assay

The T7E1 assay was used to detect mutation events in genomic DNA such as insertions, deletions and substitutions created through non-homologous end joining (NHEJ) following DNA cleavage by Cas9 (See Cho et al., Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease. Nature Biotechnology. 2013; 31, 230-232).

Genomic DNA regions that have been targeted for cutting by CRISPR/Cas9 were amplified by PCR, denatured at 95° C. for 10 minutes, and then re-annealed by ramping down from 95° C. to 25° C. at 0.5° C. per second. If mutations were present within the amplified region, the DNA combined to form heteroduplexes. The re-annealed heteroduplexes were then digested with T7E1 (New England Biolabs) at 37° C. for 25 minutes or longer. T7E1 endonuclease recognizes DNA mismatches, heteroduplexes and nicked double stranded DNA and generates a double stranded break at these sites. The resulting DNA fragments were analyzed using a Fragment Analyzer and quantified to determine cleavage efficiency.

Next-Generation Sequencing (NGS) and Analysis for On-Target Cleavage Efficiency and Indel Formation

To determine the efficiency of editing (e.g., cleaving) the target location in the genome, deep sequencing was utilized to identify the presence of insertions and deletions introduced by non-homologous end joining.

PCR primers were first designed around the target site, and the genomic area of interest PCR amplified. Additional PCR was performed according to manufacturer's protocols (Illumina) to add the necessary chemistry for sequencing. The amplicons were then sequenced on an Illumina MiSeq instrument. The reads were then aligned to the human reference genome (e.g., hg38) after eliminating those having low quality scores. From the resulting files containing the reads mapped to the reference genome (BAM files), reads which overlap the target region of interest were selected and the number of wild type reads versus the number of reads which contain an insertion or deletion was calculated. The editing percentage was then defined as the total number of reads with insertions or deletions over the total number of reads, including wild type. To determine the pattern of insertions and/or deletions that resulted from the edit, the aligned reads with indels were selected and the number of a reads with a given indel were summed. This information was then displayed as a list as well as visualized in the form on histograms which represent the frequency of each indel.

RNP Generation

The addition of crRNA and trRNA to Cas9 protein results in the formation of the active Cas9 ribonucleoprotein complex (RNP), which mediates binding to the target region specified by the crRNA and specific cleavage of the targeted genomic DNA. This complex was formed by loading trRNA and crRNA into Cas9, which is believed to cause conformational changes to Cas9 allowing it to bind and cleave dsDNA.

The crRNA and trRNA were separately denatured at 95° C. for 2 minutes, and allowed to come to room temperature. Cas9 protein (10 mg/ml) was added to 5×CCE buffer (20 mM HEPES, 100 mM KCl, 5 mM MgCl₂, 1 mM DTT, 5% glycerol), to which trRNA and the various crRNAs were then added (in separate reactions) and incubated at 37° C. for 10 minutes, thereby forming the active RNP complex. The complex was delivered by electroporation and other methods into a wide variety of cells, including HEK-293 and CD34+ hematopoietic cells.

Delivery of RNPs to CD34+ HSCs

Cas9 RNPs were delivered into CD34+ HSCs.

CD34+ HSCs were thawed and cultured (at 500,000 cells/ml) overnight in StemSpan SFEM (StemCell Technologies) media with IL12, SCF, TPO, Flt3L and Pen/Strep added. Roughly 90,000 cells were aliquoted and pelleted per each RNP delivery reaction. The cells were then resuspended in 60 ul P3 nucleofection buffer (Lonza), to which active RNP was subsequently added. The HSCs were then electroporated (e.g., nucleofected using program CA-137 on a Lonza Nucleofector) in triplicate (20 uL/electroporation). Immediately following electroporation, StemSpan SFEM media (with IL12, SCF, TPO, Flt3L and Pen/Strep) was added to the HSCs, which were cultured for at least 24 hours. HSCs were then harvested and subjected to T7E1, NGS, and/or surface marker expression analyses.

HSC Functional Assay

CD34+ HSCs may be assayed for stem cell phenotype using known techniques such as flow cytometry or the in vitro colony forming assay. By way of example, cells were assayed by the in vitro colony forming assay (CFC) using the Methocult H4034 Optimum kit (StemCell Technologies) using the manufacturer's protocol. Briefly, 500-2000 CD34+ cells in <=100 ul volume are added to 1-1.25 ml methocult. The mixture was vortexed vigorously for 4-5 seconds to mix thoroughly, then allowed to rest at room temperature for at least 5 minutes. Using a syringe, 1-1.25 ml of MethoCult+ cells was transferred to a 35 mm dish or well of a 6-well plate. Colony number and morphology was assessed after 12-14 days as per the manufacturer's protocol.

In Vivo Xeno-Transplantation

HSCs are functionally defined by their ability to self-renew and for multi-lineage differentiation. This functionality can only be assessed in vivo. The gold-standard for determining human HSC function is through xeno-transplantation into the NOD-SCID gamma mouse (NSG) that through a series of mutations is severely immunocompromised and thus can act as a recipient for human cells. HSCs following editing will be transplanted into NSG mice to validate that the induced edit does not impact HSC function. Monthly peripheral blood analysis will be used to assess human chimerism and lineage development and secondary transplantation following 20 weeks will be used to establish the presence of functional HSCs.

Results

The results of editing using gRNA molecules (e.g., dgRNA molecules as describe above) described herein, in HEK293_Cas9GFP cells, as assayed by T7E1 (“T7”) and/or NGS are summarized in FIG. 1 (gRNAs molecules to +58 BCL11a enhancer region) and FIG. 2 (gRNA moleucles to +62 BCL11a enhancer region), and in the tables below, as indicated. Average editing in CD34+ HSPCs are reported in, for example, Table 10 (gRNAs molecules to +58 BCL11a enhancer region), Table 11 (gRNAs molecules to +62 BCL11a enhancer region), Table 12B (gRNAs molecules to +55 BCL11a enhancer region), and Table 13 (gRNAs molecules to the French HPFH region), below. Where T7E1 assay results are reported, “2” indicates high efficiency cutting; “1” indicates low efficiency cutting, and “0” indicates no cutting. In general, T7E1 results correlate with the quantitative cutting assayed by NGS. Top 15 gRNAs (as ranked by highest % editing in CD34+ cells) are shown in FIG. 11 (+58 BCL11a enhancer region) and FIG. 12 (+62 BCL11a enhancer region).

TABLE 10 Bcl11a +58 enhancer region crRNA 1° Screen results in CD34+ HSPCs (by NGS, n = 3). Average % Targeting Domain Editing ID (n = 3) StDev CR000242 1.4% 0.3% CR000243 n/a n/a CR000244 3.7% 1.0% CR000245 24.7% 1.4% CR000246 24.2% 0.3% CR000247 3.6% 0.6% CR000248 6.4% 0.5% CR000249 13.3% 0.6% CR000250 4.8% 0.5% CR000251 4.7% 0.5% CR000252 2.7% 0.5% CR000253 9.0% 0.6% CR000255 n/a n/a CR000256 1.3% 0.2% CR000257 2.4% 0.4% CR000258 2.0% 0.0% CR000259 3.9% 0.4% CR000260 32.7% 2.3% CR000261 17.9% 0.9% CR000264 2.1% 0.2% CR000266 2.9% 0.1% CR000267 3.9% 0.1% CR000268 6.3% 0.6% CR000269 4.4% 0.2% CR000270 2.7% 0.9% CR000271 7.2% 1.4% CR000272 11.9% 2.9% CR000273 3.1% 0.2% CR000274 1.4% 0.1% CR000275 9.6% 0.6% CR000276 14.5% 0.5% CR000277 8.6% 0.5% CR000278 4.8% 0.6% CR000279 6.5% 0.9% CR000280 7.9% 0.8% CR000281 3.3% 0.7% CR000282 10.1% 1.2% CR000283 4.7% 0.2% CR000284 5.8% 0.1% CR000285 8.9% 1.2% CR000286 20.2% 1.1% CR000287 10.1% 1.0% CR000288 1.6% 0.1% CR000289 3.0% 0.4% CR000290 2.3% 0.4% CR000291 2.8% 0.1% CR000292 9.9% 0.9% CR000293 n/a n/a CR000294 2.7% 0.5% CR000295 1.9% 0.4% CR000296 2.8% 0.4% CR000297 5.7% 0.4% CR000298 2.2% 0.2% CR000299 2.9% 0.2% CR000300 2.3% 0.2% CR000301 10.2% 0.8% CR000302 5.0% 0.6% CR000303 3.7% 0.3% CR000304 6.2% 0.8% CR000305 7.7% 2.2% CR000306 4.0% 2.2% CR000307 8.8% 3.6% CR000308 39.9% 1.7% CR000309 38.3% 8.2% CR000310 56.8% 1.0% CR000311 46.0% 1.2% CR000312 48.5% 1.7% CR000313 41.2% 4.4% CR000314 29.9% 0.9% CR000315 32.0% 2.9% CR000316 3.9% 1.0% CR000317 2.8% 0.3% CR000318 2.6% 0.2% CR000319 7.9% 1.8% CR000320 1.9% 0.1% CR000321 13.2% 1.7% CR000322 5.2% 0.8% CR000323 20.3% 2.1% CR000324 2.2% 0.4% CR000325 8.4% 0.9% CR000326 1.4% 0.2% CR000327 6.9% 1.7% CR000328 2.6% 0.4% CR000329 1.1% 0.1% CR000330 1.7% 0.2% CR000331 22.0% 0.9% CR000332 3.2% 1.0% CR000333 3.8% 0.7% CR000334 3.2% 0.1% CR000335 2.7% 0.3% CR000336 2.2% 0.2% CR000337 7.2% 1.0% CR000338 10.3% 1.8% CR000339 4.2% 0.2% CR000340 4.6% 0.6% CR000341 7.5% 1.4% CR001124 26.1% 2.0% CR001125 8.4% 1.6% CR001126 17.2% 5.8% CR001127 7.4% 2.3% CR001128 9.0% 0.9% CR001129 16.5% 6.0% CR001130 11.1% 8.3% CR001131 54.1% 4.9%

TABLE 11 Bcl11a +62 enhancer region crRNA 1° Screen results in CD34+ HSPCs (by NGS, n = 3). Average % Targeting Domain ID Edit (n = 3) StDev CR000171 4.4 0.7 CR000172 4.6 2.4 CR000173 3.1 0.7 CR000174 27.6 6.5 CR000175 14.7 1.0 CR000176 2.1 0.6 CR000177 7.6 2.3 CR000178 7.1 1.7 CR000179 7.7 1.8 CR000180 2.8 0.5 CR000181 25.6 3.8 CR000182 27.6 3.5 CR000183 30.5 6.9 CR000184 4.2 1.9 CR000185 11.4 0.7 CR000186 7.2 3.7 CR000187 46.3 2.2 CR000188 21.0 6.0 CR000189 22.3 2.1 CR000190 20.2 5.7 CR000191 38.2 7.9 CR000192 5.4 1.8 CR000193 14.7 2.0 CR000194 13.5 0.7 CR000195 8.2 1.2 CR000196 27.0 6.4 CR000197 6.6 0.6 CR000198 8.7 3.2 CR000199 3.3 1.3 CR000200 6.9 0.5 CR000201 1.6 0.5 CR000202 28.1 5.6 CR000203 43.7 0.5 CR000204 35.1 2.2 CR000205 53.6 0.8 CR000206 52.8 6.0 CR000207 2.5 0.3 CR000208 31.5 7.5 CR000209 13.5 2.9 CR000210 28.7 6.6 CR000211 59.3 5.5 CR000212 40.0 1.6 CR000213 13.6 7.1 CR000214 9.4 0.7 CR000215 37.0 6.9 CR000216 25.3 2.6 CR000217 7.6 1.6 CR000218 5.1 1.3 CR000221 12.4 3.5 CR000222 7.2 2.6 CR000223 8.4 2.1 CR000224 13.9 5.3 CR000225 10.3 4.4 CR000227 12.6 1.8 CR000228 13.5 4.8 CR000229 3.2 0.8

TABLE 12A Bcl11a +55 enhancer region crRNA 1° Screen results in HEK-293-Cas9 Cells Targeting Domain Average % Edit ID (n = 3) StDev CR002142 25.0 2.0 CR002143 n/a n/a CR002144 51.2 8.3 CR002145 51.0 3.3 CR002146 n/a n/a CR002147 n/a n/a CR002148 13.7 4.3 CR002149 22.3 4.5 CR002150 43.8 9.0 CR002151 31.1 0.6 CR002152 33.2 8.7 CR002153 24.5 7.8 CR002154 62.1 3.9 CR002155 48.2 10.9  CR002156 57.4 8.5 CR002157 46.6 4.3 CR002158 11.0 1.7 CR002159 13.7 2.3 CR002160 37.8 0.8 CR002161 61.5 4.6 CR002162 47.0 14.0  CR002163 52.2 9.6 CR002164 58.5 4.4 CR002165 61.5 6.8 CR002166 42.6 11.3  CR002167 37.8 4.7 CR002168 32.0 12.9  CR002169 48.5 6.3 CR002170 44.8 2.9 CR002171 n/a n/a CR002172 n/a n/a CR002173 n/a n/a CR002174 59.8 3.8 CR002175 22.1 1.3 CR002176 35.4 5.9 CR002177 n/a n/a CR002178 25.9 3.2 CR002179 n/a n/a CR002180 57.6 6.4 CR002181 63.8 3.9 CR002182 n/a n/a CR002183 n/a n/a CR002184 30.0 4.0 CR002185 n/a n/a CR002186 n/a n/a CR002187 51.6 2.9 CR002188 35.8 8.7 CR002189 62.7 6.0 CR002190 n/a n/a CR002191 37.4 7.4 CR002192 n/a n/a CR002193 6.1 1.7 CR002194 n/a n/a CR002195 60.0 9.4 CR002196 42.9 13.7  CR002197 52.2 2.8 CR002198 n/a n/a CR002199 n/a n/a CR002200  4.3 1.0 CR002201  1.8 0.3 CR002202  2.6 0.3 CR002203 50.7 5.3 CR002204 n/a n/a CR002205 n/a n/a CR002206 n/a n/a CR002207 n/a n/a CR002208 n/a n/a CR002209 n/a n/a CR002210 n/a n/a CR002211 n/a n/a CR002212 n/a n/a CR002213 n/a n/a CR002214 n/a n/a CR002215 51.7 8.9 CR002216 14.1 8.3 CR002217 50.1 10.5  CR002218 45.0 19.4  CR002219 30.7 14.7  CR002220 44.7 13.3  CR002221 n/a n/a CR002222 64.0 3.9 CR002223 n/a n/a CR002224 n/a n/a CR002225 n/a n/a CR002226 n/a n/a CR002227 n/a n/a CR002228 10.4 5.6 CR002229 n/a n/a n/a = not assessed

After the experiment above, the same guide RNA molecules were tested again in triplicate in both HEK-293-Cas9 cells and in CD34+ cells using a newly designed set of primers for the NGS analysis. The results are reported below in Table 12B.

TABLE 12B Bcl11a +55 enhancer region crRNA screen results in HEK-293-Cas9 Cells and in CD34+ HSPCs (by NGS, n = 3). Editing % HEK- Editing % 293-Cas9 Cells CD34+ HSPCs ID (n = 3) (n = 3) CR002142 2.1 2.07 CR002143 39.6 2.31 CR002144 74.3 4.70 CR002145 72.1 11.46 CR002146 77.2 5.18 CR002147 37.3 3.13 CR002148 34.6 2.02 CR002149 40.7 3.16 CR002150 64.4 4.01 CR002151 70.5 5.05 CR002152 63.6 6.59 CR002153 42.2 2.82 CR002154 71.0 17.89 CR002155 60.3 6.01 CR002156 62.3 9.43 CR002157 38.5 4.72 CR002158 12.4 2.16 CR002159 14.8 3.64 CR002160 72.8 7.97 CR002161 74.5 18.12 CR002162 64.8 4.53 CR002163 86.7 13.92 CR002164 3.2 10.23 CR002165 78.3 9.74 CR002166 67.2 7.78 CR002167 51.6 29.26 CR002168 29.9 4.15 CR002169 80.2 9.11 CR002170 83.0 16.17 CR002171 67.8 4.83 CR002172 64.3 7.59 CR002173 80.7 6.00 CR002174 78.2 26.89 CR002175 79.4 27.08 CR002176 39.5 5.14 CR002177 66.7 21.45 CR002178 52.5 12.74 CR002179 83.1 38.88 CR002180 51.3 5.46 CR002181 54.0 12.54 CR002182 67.9 28.01 CR002183 30.3 3.52 CR002184 67.1 21.31 CR002185 65.6 8.18 CR002186 58.9 8.16 CR002187 70.2 10.05 CR002188 56.6 9.92 CR002189 71.9 31.14 CR002190 27.4 6.84 CR002191 70.0 17.54 CR002192 62.6 6.92 CR002193 1.6 0.67 CR002194 82.5 24.52 CR002195 64.4 36.32 CR002196 2.1 0.96 CR002197 63.8 37.29 CR002198 67.8 16.45 CR002199 61.3 9.78 CR002200 3.1 1.10 CR002201 1.2 0.84 CR002202 2.8 0.82 CR002203 49.9 0.84 CR002204 43.2 17.48 CR002205 60.6 11.06 CR002206 48.5 9.02 CR002207 49.4 12.29 CR002208 61.7 16.56 CR002209 61.2 9.36 CR002210 57.6 27.77 CR002211 45.4 30.93 CR002212 56.0 31.55 CR002213 34.4 10.40 CR002214 11.1 1.77 CR002215 49.3 40.23 CR002216 22.1 1.80 CR002217 52.3 11.29 CR002218 73.7 11.17 CR002219 34.2 7.94 CR002220 64.8 8.63 CR002221 20.7 5.66 CR002222 78.9 30.01 CR002223 8.2 1.21 CR002224 7.8 n.d CR002225 n.d n.d CR002226 2.6 n.d CR002227 n.d n.d CR002228 23.2 3.65 CR002229 39.0 n.d n.d. = not determined

TABLE 13 French HPFH region crRNA 1° Screen results in HEK-293-Cas9 Cells and in CD34+ HSPCs (by NGS, n = 3). Average Edit % Average Edit % StDev (%) for Targeting HEK-293-Cas9 CD34+ HSPCs % Edit in Domain ID (n = 3) (n = 3) CD34+ HSPCs CR001016 33.1 24.0 1.2 CR001017 30.4 19.5 1.5 CR001018 46.5 53.0 3.4 CR001019 45.9 57.6 2.3 CR001020 62.1 47.7 9.3 CR001021 29.1 34.2 1.8 CR001022 66.1 66.2 2.3 CR001023 27.3 46.0 6.1 CR001024 62.5 73.4 6.9 CR001025 25.5 24.5 1.6 CR001026 61.4 72.1 2.9 CR001027 23.3 33.2 2.2 CR001028 47.7 72.1 4.9 CR001029 53.9 61.2 5.7 CR001030 49.2 49.9 29.0 CR001031 42.7 65.0 9.3 CR001032 67.6 50.1 9.7 CR001033 15.3 44.5 3.2 CR001034 28.5 52.9 2.7 CR001035 16.9 28.5 16.4 CR001036 28.0 68.3 3.7 CR001037 52.7 53.2 4.2 CR001038 1.9 23.7 20.6 CR001039 2.2 35.8 2.8 CR001040 nd n/a 0.0 CR001041 nd n/a 0.0 CR001042 2.7 n/a 0.0 CR001043 nd n/a 0.0 CR001044 4.9 1.5 0.4 CR001045 38.1 31.2 2.0 CR001046 18.4 28.4 3.9 CR001047 nd n/a 0.0 CR001048 1.6 0.2 0.3 CR001049 nd n/a 0.0 CR001050 nd n/a 0.0 CR001051 nd n/a 0.0 CR001052 nd n/a 0.0 CR001053 5.8 4.4 0.7 CR001054 9.0 4.1 0.4 CR001055 5.2 0.1 0.1 CR001056 7.7 5.0 0.3 CR001057 25.2 7.8 0.8 CR001058 41.6 29.5 6.7 CR001059 5.2 4.9 0.1 CR001060 43.5 18.7 5.2 CR001061 21.7 4.7 0.8 CR001062 12.2 5.2 1.1 CR001063 16.6 21.5 1.6 CR001064 6.0 4.2 0.7 CR001065 43.0 20.0 1.4 CR001066 11.1 4.2 0.4 CR001067 25.7 7.9 3.5 CR001068 11.3 5.9 1.6 CR001069 15.1 2.9 0.2 CR001070 38.2 11.1 3.1 CR001071 34.6 8.5 0.2 CR001072 22.8 3.5 0.4 CR001073 45.2 18.1 4.1 CR001074 40.1 38.1 2.5 CR001075 53.0 29.2 1.8 CR001076 25.6 1.8 0.1 CR001077 8.9 12.2 0.4 CR001078 10.9 17.7 3.3 CR001079 18.3 7.8 0.9 CR001080 21.3 17.4 5.6 CR001081 22.0 21.4 0.5 CR001082 5.4 8.5 0.6 CR001083 12.3 11.6 0.5 CR001084 25.4 9.5 4.5 CR001085 18.3 12.4 1.7 CR001086 25.3 4.4 2.0 CR001087 16.4 6.9 0.9 CR001088 9.6 18.4 1.9 CR001089 nd 15.8 12.9 CR001090 16.9 30.1 3.5 CR001091 11.4 0.8 0.5 CR001092 17.4 17.0 9.8 CR001093 23.0 13.0 4.5 CR001094 10.0 24.9 5.4 CR001095 22.1 34.8 3.6 CR001096 29.8 20.4 2.0 CR001097 17.9 20.5 0.5 CR001098 49.8 34.7 5.1 CR001099 24.7 39.9 1.8 CR001100 nd 33.2 2.8 CR001101 16.9 24.7 2.1 CR001102 29.4 13.9 0.7 CR001103 9.9 8.6 2.2 CR001104 11.3 3.3 0.7 CR001105 5.0 3.6 0.9 CR001106 15.7 13.1 1.6 CR001107 31.2 8.5 4.5 CR001108 16.1 3.2 0.5 CR001109 12.1 4.6 2.1 CR001110 23.5 6.0 3.0 CR001111 12.3 2.6 1.3 CR001132 18.7 3.4 0.4 CR001133 35.4 27.0 4.2 CR001134 12.3 0.3 0.2 CR001135 57.8 16.2 2.7 CR001136 7.1 1.7 0.5 CR001137 31.2 6.2 2.7 CR001138 45.4 9.6 1.2 CR001139 nd 3.3 0.3 CR001140 28.7 11.2 1.2 CR001141 3.6 1.5 0.5 CR001142 56.7 9.7 1.2 CR001143 58.4 4.6 1.3 CR001144 23.2 4.3 2.5 CR001145 4.9 0.1 0.0 CR001146 38.2 0.2 0.0 CR001147 16.0 0.1 0.1 CR001148 22.3 3.0 1.6 CR001149 19.4 6.0 3.9 CR001150 30.8 30.4 17.9 CR001151 35.8 0.8 0.2 CR001152 24.6 0.3 0.1 CR001153 5.4 0.3 0.4 CR001154 6.3 3.6 2.1 CR001155 nd 2.1 0.6 CR001156 19.6 4.8 0.8 CR001157 16.4 2.7 0.6 CR001158 36.5 5.1 3.2 CR001159 42.9 7.7 1.0 CR001160 32.5 8.5 1.9 CR001161 20.5 10.3 1.9 CR001162 35.0 30.5 4.5 CR001163 9.9 3.3 0.5 CR001164 23.3 14.4 8.8 CR001165 5.5 1.5 0.4 CR001166 49.8 27.1 4.4 CR001167 13.8 6.0 0.8 CR001168 nd 6.4 4.7 CR001169 43.9 n/a 0.0 CR001170 28.5 10.7 6.4 CR001171 37.5 2.7 2.6 CR001172 41.5 14.8 3.5 CR001173 49.5 16.7 3.9 CR001174 36.6 4.4 0.7 CR001175 17.0 5.3 1.7 CR001176 7.7 3.6 2.8 CR001177 4.0 4.1 2.3 CR001178 nd 27.0 15.6 CR001179 59.0 27.9 1.5 CR001180 nd 8.5 5.3 CR001181 30.9 5.7 0.8 CR001182 34.5 13.6 7.8 CR001183 6.9 0.4 0.3 CR001184 15.7 5.2 2.7 CR001185 18.2 7.6 1.2 CR001186 12.0 5.0 0.6 CR001187 8.3 4.1 0.3 CR001188 16.8 7.1 2.0 CR001189 13.3 3.7 1.3 CR001190 nd 5.6 1.1 CR001191 39.5 4.8 1.0 CR001192 27.5 3.9 1.3 CR001193 17.1 1.5 1.9 CR001194 17.8 5.9 4.1 CR001195 nd 16.4 9.5 CR001196 5.8 2.2 0.7 CR001197 32.4 8.1 3.1 CR001198 28.4 18.2 5.8 CR001199 40.8 7.9 4.0 CR001200 24.4 1.2 0.7 CR001201 1.7 0.3 0.1 CR001202 46.0 39.3 22.7 CR001203 11.9 3.1 1.6 CR001204 1.2 0.8 0.1 CR001205 3.0 0.2 0.1 CR001206 3.9 0.5 0.2 CR001207 7.6 2.4 1.2 CR001208 5.5 1.5 0.7 CR001209 4.4 1.7 0.2 CR001210 10.8 3.9 2.5 CR001211 6.8 3.4 2.0 CR001212 32.7 11.1 6.5 CR001213 21.6 6.2 1.5 CR001214 28.4 5.7 0.8 CR001215 9.0 1.5 0.5 CR001216 nd 2.5 1.4 CR001217 nd n/a 0.0 CR001218 7.7 4.1 1.0 CR001219 40.0 20.3 0.6 CR001220 33.8 n/a 0.0 CR001221 41.3 n/a 0.0 CR001222 39.1 18.9 10.9 CR001223 35.9 n/a 0.0 CR001224 34.9 16.5 7.1 CR001225 55.0 24.6 1.1 CR001226 34.1 4.7 4.1 CR001227 46.4 6.4 0.6 CR003027 50.2 4.5 nd CR003028 3.0 2.2 nd CR003029 14.4 3.4 nd CR003030 20.2 5.8 nd CR003031 31.3 9.7 nd CR003032 15.1 4.4 nd CR003033 46.5 25.2 nd CR003034 55.2 11.8 nd CR003035 42.4 15.9 nd CR003036 17.4 6.1 nd CR003037 38.6 19.6 nd CR003038 47.1 24.6 nd CR003039 53.8 21.1 nd CR003040 35.9 6.1 nd CR003041 23.7 9.9 nd CR003042 35.5 8.7 nd CR003043 24.4 4.3 nd CR003044 54.1 16.2 nd CR003045 33.7 6.6 nd CR003046 34.8 3.6 nd CR003047 46.9 9.8 nd CR003048 12.6 1.7 nd CR003049 24.4 4.9 nd CR003050 19.6 2.9 nd CR003051 15.4 1.8 nd CR003052 15.7 7.8 nd CR003053 10.8 0.9 nd CR003054 16.7 2.9 nd CR003055 17.3 4.4 nd CR003056 46.3 19.3 nd CR003057 40.9 11.3 nd CR003058 40.0 8.9 nd CR003059 23.7 <2% nd CR003060 16.8 <2% nd CR003061 27.6 <2% nd CR003062 3.9 <2% nd CR003063 19.8 2.5 nd CR003064 19.6 <2% nd CR003065 42.3 0.1 nd CR003066 36.5 0.0 nd CR003067 53.1 0.1 nd CR003068 11.5 <2% nd CR003069 42.7 0.0 nd CR003070 49.0 0.1 nd CR003071 41.8 <2% nd CR003072 27.2 <2% nd CR003073 45.1 0.1 nd CR003074 40.2 0.1 nd CR003075 58.5 0.1 nd CR003076 28.5 <2% nd CR003077 44.9 0.0 nd CR003078 43.9 <2% nd CR003079 31.1 <2% nd CR003080 41.1 <2% nd CR003081 29.4 <2% nd CR003082 30.8 <2% nd CR003083 26.5 0.0 nd CR003084 32.3 <2% nd CR003085 24.0 0.1 nd CR003086 40.8 10.8 nd CR003087 51.0 45.0 nd CR003088 25.5 9.7 nd CR003089 26.0 11.5 nd CR003090 15.2 <2% nd CR003091 26.4 5.5 nd CR003092 4.9 2.1 nd CR003093 16.7 2.9 nd CR003094 39.5 4.7 nd CR003095 12.0 1.7 nd CR003096 22.9 4.0 nd n/a = not assayed; nd = not determined

Genome Editing at the BCL11a Enhancer Site

Synthetic sgRNA molecules containing targeting domains specific for genomic DNA within the +58 or +62 erythroid enhancer region of BCL11a were ordered. FIG. 5 shows the genomic DNA targeted by the sgRNAs, which were named sgEH1 through sgEH9.

sgEH1 Targeting Domain (CR00276): (SEQ ID NO: 212) AUCACAUAUAGGCACCUAUC sgEH2 Targeting Domain (CR00275): (SEQ ID NO: 211) CACAGUAGCUGGUACCUGAU sgEH8 Targeting Domain (CR00273): (SEQ ID NO: 209) CAGGUACCAGCUACUGUGUU sgEH9 (CR00277) Targeting Domain: (SEQ ID NO: 213) UGAUAGGUGCCUAUAUGUGA

RNPs containing sgEH[X] precomplexed with Cas9 were introduced into CD34+ bone marrow cells (Bone Marrow CD34+ cells ordered from Lonza, Cat #2M-101C, Lot#466977, 30y, F, B (96.8%)) using electroporation (NEON electroporator). Cutting was determined in CD34+ stem cells using T7E1 and NGS. The results are summarized in FIG. 6A-D, which shows overall indel formation across four experiments (two experiments from two different donors), as well as the top indel patterns. sgEH1, 2 and 9 were able to direct cutting with high efficiency.

It was surprisingly found that across multiple experiments, including those using cells from different donors, the indel pattern remained constant (See FIG. 6A-D). That is, each gRNA gave a consistent pattern of indel formation. As well, deletions appeared to correlate with regions of microhomology near the cutting site.

To further investigate this phenomenon, gRNAs to the BCL11a locus were designed at tested using different biological samples as well as different delivery methods, and gRNA scaffolds. For this experiment, gRNAs with the following targeting domains were used:

G7 (also referred to as g7) Targeting domain: GUGCCAGAUGAACUUCCCAU (e.g., the 3′ 20 nt of SEQ ID NO: 1191) G8 (also referred to as g8) Targeting domain: CACAAACGGAAACAAUGCAA (e.g., the 3′ 20 nt of SEQ ID NO: 1186)

In a first experiment, g7 and g8 were tested across two different biological samples. As shown in FIG. 7, the pattern of top 3 most prevalent indels for each gRNA was identical. Next, gRNA molecules comprising the G7 and G8 targeting domains were tested with a different tracrRNA component. In the previous experiments, SEQ ID NO: 6601, followed by -UUUU, was directly appended to the gRNA targeting domain to form the sgRNA. In the next set of experiments, SEQ ID NO: 6604, followed by -UUUU, was directly appended to the gRNA targeting domains of g7 and g8 to create sgRNA molecules with a different scaffold (gRNAs called g7BC or g8BC). As shown in FIG. 8, the indel pattern remained constant even when different sgRNA scaffolds are used. Finally, the indel pattern was compared using different delivery methods. Delivery of g7 to 293 cells via either RNP electroporation or by delivery of a g7-encoding plasmid via lipofectamine 2000 was investigated and the results reported in FIG. 9. As shown, the indel pattern remained the same.

Together, these results strongly suggest that indel pattern formation is sequence-dependent. gRNA molecules that target sequences where cutting results in large deletions and/or frameshift deletions may be beneficial for loss of function.

Excision with Multiple Guides

G7 and g8, above, target genomic DNA at proximal sites (PAM sequences are within 50 nucleotides of each other within the BCL11a gene). To investigate the effect of simultaneously targeting two proximal sites, CD34+ cells were transfected with RNPs comprising gRNAs with the targeting domain of G7 as well as RNPs comprising gRNAs with the targeting domain of G8. Cutting efficiency and indel pattern was assessed by NGS. As shown in FIG. 10, the primary indel is a delection of the nucleotides between the two gRNA binding sites. These results demonstrate that a plurality, e.g., 2, guides that bind in proximity may be used to effect an excision of the DNA located between the two binding sites.

Genome Editing in CD34+ Stem Cells

Genome editing at the BCL11a locus was demonstrated in CD34+ primary hematopoietic stem cells. Briefly, CD34+ cells were isolated from G-CSF mobilized peripheral blood from adult donors (AllCells) using immunoselection (Miltenyi) according to the manufacturer's instructions. Cell gating is shown in FIG. 3. Cells were aliquotted and cryopreserved. Thawed cells were seeded at 2×10⁵/ml in SFEM (StemCell Technologies)+1× antibiotic/antimycotic+50 ng/ml each cytokine (TPO, FLT3L, IL6 and SCF)+500 nM compound 4 and cultured for 5 days at 37 C, 5% CO2 in a humidified incubator. Cell concentration after 5 days was 1×10⁶/ml.

Preincubated RNP complex consisting of 150 ng each Cas9 (Genscript #265425-7) and sgRNA (TriLink, comprising the sgBCL11A_7 Targeting Domain (i.e., the targeting domain of g7): GTGCCAGATGAACTTCCCATGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAAT AAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTT) (SEQ ID NO: 2000) was added to 2×10⁵ cells and electroporated on the Neon system (Lifetechnologies) with pulse parameters: 1600 V, 20 ms, 1 pulse, according to manufacturer's protocols. Duplicate electroporation were performed. Mock electroporation were also performed in the absence of RNP complex. After electroporation, cells were seeded into 1 ml media to recover overnight.

The day following electroporation, 1/20 of the unsorted culture was seeded in SFEM (StemCell Technologies)+1× antibiotic/antimycotic+50 ng/ml each TPO, FLT3L, IL6, SCF, IL3 and GCSF for 6 days. The remaining cells were stained with antibodies to human CD34 and human CD90 and sorted by flow cytometry for CD34+CD90+ and CD34+CD90− populations. CD34+CD90+ cells are known to contain hematopoietic stem cells, as defined by long-term multi-lineage engraftment in immunodeficient mice (see Majeti et al. 2007 Cell Stem Cell 1, 635-645). Cell populations selected for sorting are indicated by the gates in the representative dot plot of FIG. 3. Sorted cells were cultured in SFEM (StemCell Technologies)+1× antibiotic/antimycotic+50 ng/ml each TPO, FLT3L, IL6, SCF, IL3 and GCSF for 6 days, at which point all cultures were harvested for analysis of genome editing.

Genomic DNA was purified from harvested cells and the targeted region was amplified with the following primers: BCL11A-7 F, gcttggctacagcacctctga; BCL11A-7 R, ggcatggggttgagatgtgct. PCR product was denatured and reannealed, followed by incubation with T7E1 (New England Biolabs) as per the manufacturer's recommendations. The reaction was then analyzed by agarose gel electrophoresis (FIG. 4). The upper band represents uncleaved homoduplex DNA and the lower bands indicate cleavage products resulting from heteroduplex DNA. The far left lane is a DNA ladder. Band intensity was calculated by peak integration of unprocessed images by ImageJ software. % gene modification (indel) was calculated as follows: % gene modification=100×(1−(1−fraction cleaved)^(1/2)), and is indicated below each corresponding lane of the gel.

The results are shown in FIG. 4. Gene editing efficiency in the hematopoietic stem cell-containing CD34+CD90+ population was equivalent to CD34+CD90− cells or unsorted. These experiments demonstrate that gene editing can be accomplished in CD34+ HSPCs and CD34+CD90+ cells that are further enriched in HSCs.

Example 3. BCL11A Erythroid Enhancer Editing in Hematopoietic Stem and Progenitor Cells (HSPCs) Using CRISPR-Cas9 for Derepression of Fetal Globin Expression in Adult Erythroid Cells Methods:

Human CD34⁺ cell culture. Human bone marrow CD34⁺ cells were purchased from either AllCells (Cat#: ABM017F) or Lonza (Cat#: 2M-101C) and expanded for 2 to 3 days using StemSpan SFEM (StemCell Technologies; Cat no. 09650) supplemented with 50 ng/mL of thrombopoietin (Tpo, Peprotech; Cat#300-18), 50 ng/mL of human Flt3 ligand (Flt-3L, Peprotech; Cat#300-19), 50 ng/mL of human stem cell factor (SCF, Peprotech; Cat#300-07), human interleukin-6 (IL-6, Peprotech; Cat#200-06), 1% L-glutamine; 2% penicillin/streptomycin, and Compound 4 (0.75 μM). After 2 to 3 days of expansion, the culture had expanded 2- to 3-fold relative to starting cell numbers purchased from AllCells and 1- to 1.5-fold from Lonza. These culture conditions were used for all CD34+ expansion steps, including both before and after introduction of the CRISPR/Cas systems as described herein.

Assembly of Cas9 and guide RNA ribonucleoprotein (RNP) complexes, preparation of HSC, and electroporation of RNP into HSC. Cas9-guide RNA ribonucleoprotein complexes (RNPs) were prepared immediately prior to electroporation. For formation of RNP using dual guide RNAs (dgRNAs), 3 μg of each of crRNA (in 2.24 μL) and tracr (in 1.25 μL) are first denatured at 95° C. for 2 min in separate tubes and then cooled to room temperature. For preparation of Cas9 protein, 7.3 μg of CAS9 protein (in 1.21 μL) was mixed with 0.52 μL of 5×CCE buffer (20 mM HEPES, 100 mM KCL, 5 mM MgCL2, 5% Glycerol and freshly added 1 mM DTT). Tracr was first mixed with the Cas9 preparation and incubated at 37° C. for 5 min. The crRNA was then added to Tracr/CAS9 complexes and incubated for 5 min at 37° C. The HSC were collected by centrifugation at 200×g for 15 min and resuspended in T buffer that comes with Neon electroporation kit (Invitrogen; Cat#: MPK1096) at a cell density of 2×10⁷/mL. The RNP mixed with 12 μL of cells by pipetting up and down 3 times gently. To prepare single guide RNA (sgRNA) and Cas9 complexes, 2.25 μg sgRNA (in 1.5 μL) was mixed with 2.25 μg Cas9 protein (in 3 μL) and incubated at RT for 5 min. The sgRNA/Cas9 complex was then mixed with 10.5 μL of 2×10⁷/mL cells by pipetting up and down several times gently and incubated at RT for 2 min. The RNP/cell mixture (10 μL) was transferred into Neon electroporation probe. The electroporation was performed with Neon transfection system (Invitrogen; MPK5000S) using 1700 volts/20 milliseconds and 1 pulse. After electroporation, the cells were transferred into 0.5 mL pre-warmed StemSpan SFEM medium supplemented with growth factors and cytokines as described above and cultured at 37° C. for 2 days.

Genomic DNA preparation. Genomic DNA was prepared from edited and unedited HSC at 48 hours post-electroporation. The cells were lysed in 10 mM Tris-HCL, pH 8.0; 0.05% SDS and freshly added Protease K of 25 μg/mL and incubated at 37° C. for 1 hour followed by additional incubation at 85° C. for 15 min to inactivate protease K.

T7E1 assay. To determine editing efficiency of HSCs, T7E1 and assay was performed. PCR was performed using Phusion Hot Start II High-Fidelity kit (Thermo Scientific; Cat#: F-549L) with the following cycling condition: 98° C. for 30″; 35 cycles of 98° C. for 5″, 68° C. for 20′, 72° C. for 30″; 72° C. for 5 min. The following primers were used: forward primer: 5′-AGCTCCAAACTCTCAAACCACAGGG-3′ (SEQ ID NO: 2001) and reverse primer: 5′-TACAATTTTGGGAGTCCACACGGCA-3′ (SEQ ID NO: 2002). The PCR products were denatured and re-annealed using the following condition: 95° C. for 5 min, 95-85° C. at −2° C./s, 85-25° C. at −0.1° C./s, 4° C. hold. After annealing, 1 μL of mismatch-sensitive T7 E1 nuclease (NEB, Cat# M0302L) was added into 10 μL of PCR product above and further incubated at 37° C. for 15 min for digestion of hetero duplexes, and the resulting DNA fragments were analyzed by agarose gel (2%) electrophoresis. The editing efficiency was quantified using ImageJ software (http://rsb.info.nih.gov/ij/).

Next generation sequencing (NGS). To determine editing efficiency more precisely and patterns of insertions and deletions (indels), the PCR products were subjected to next generation sequencing (NGS). The PCR were performed in duplicate using Titanium Taq PCR kit (Clontech Laboratories; Cat#: 639210) with the following cycling condition: 98° C. for 5 min; 30 cycles of 95° C. for 15 seconds, 68° C. for 15 seconds, 72° C. 1 min; 72° C. for 7 min. The following primers were used: forward primer: 5′-AGCTCCAAACTCTCAAACCACAGGG-3′ (SEQ ID NO: 2001) and reverse primer: 5′-TACAATTTTGGGAGTCCACACGGCA-3′ (SEQ ID NO: 2002). The PCR products were analyzed by 2% agarose gel electrophoresis and submitted for deep sequencing.

Flow cytometry analysis of HSPC culture. The HSPC were subjected to flow cytometry to characterize stem and progenitor cell populations. The percentage of CD34⁺, CD34⁺CD90⁺ cell subsets, prior to and after genome editing was determined on aliquots of the cell cultures. The cells were incubated with anti-CD34 (BD Biosciences, Cat#555824), anti-CD90 (Biolegend, Cat#328109) in staining buffer, containing PBS supplemented with 0.5% BSA, at 4° C., in dark for 30 min. The cell viability is determined by 7AAD. The cells were washed with staining buffer and Multicolor FACS analysis was performed on a FACSCanto (Becton Dickinson). Flow cytometry results analyzed using Flowjo and the data were presented as percent CD34⁺, CD34⁺CD90⁺ of the total cell population. Absolute numbers of each cell type population in the culture were calculated from the total number of cells multiplied by the percentage of each population.

In vitro erythropoiesis and FACS analysis for HbF containing erythroid cells. The genome edited HSC were subjected to in vitro erythroid differentiation 48 hours post-electroporation. Briefly, the edited HSC were cultured in erythroid differentiation medium (EDM) consisting of IMDM (Invitrogen, Cat#31980-097) supplemented with 330 μg/mL human holo-transferrin (Sigma, Cat# T0665), 10 μg/mL recombinant human insulin (Sigma, Cat#13536), 2 IU/mL heparin (Sigma, Cat # H3149), 5% human plasma (Sigma, Cat# P9523), 3 IU/mL human erythropoietin (R&D, Cat#287-TC), 1% L-glutamine, and 2% penicillin/streptomycin. During days 0-7 of culture, EDM was further supplemented with 10⁻⁶M hydrocortisone (Sigma, Cat# H0888), 100 ng/mL human SCF (Peprotech, Cat#300-07), and 5 ng/mL human IL-3 (Peprotech, Cat#200-03) for 7-days. During days 7-11 of culture, EDM was supplemented with 100 ng/mL of human SCF only. During days 11-21 of culture, EDM has no additional supplements. On days 7, 14 and 21 of the culture, the cells (2-10×10⁵) were analyzed by intracellular staining for HbF expression. Briefly, the cells were collected by centrifugation at 350×g for 5 min and washed once with staining buffer (Biolegend, Cat#420201). The cells were then fixed with 0.5 mL of fixation buffer (Biolegend, Cat#420801) and washed three times with 2 mL of 1× intracellular staining permeabilization wash buffer (Biolegend, Cat#421002) by centrifugation at 350×g for 5 min. The cells were then incubated with 5 μL of anti-HbF antibody (Life technologies, Cat# MHFH01) in 100 μL of 1× intracellular staining perm wash buffer for 20 min at room temperature. The cells were washed twice with 2 mL of 1× intracellular staining Perm wash buffer and resuspend in 200 μL staining buffer and analyzed on FACS Canto (Becton Dickinson) for HbF expression. The results analyzed using Flowjo and data were presented as % of HbF positive cells (F-cells) in total cell population.

Gene expression assays. ˜1×10⁶ cells were used to purify RNA using RNeasy mini kit (Qiagen. Cat#74104). 200 to 400 ng RNA was used for 1^(st) strand synthesize using qScript cDNA synthesis kit (Quanta, Cat#95047-500). Taq-man PCR was performed using Taq-Man Fast Advance PR Mix (Life technologies, Cat#4444963) and GAPDH (Life technologies, ID# Hs02758991_g1), HbB (Life technologies, ID#: Hs00747223_g1), HbG2/HbG1 (Life technologies, ID# Hs00361131_g1) and BCL11A (Life technologies, ID#: Hs01093197_m1) according to suppliers protocol. The relative expression of each gene was normalized to GAPDH expression.

Colony forming unit cell assay. For colony forming unit (CFU) assay, 300 cells per 1.1 mL Methocult/35 mm dish in duplicate were plated in Methocult H4434 methylcellulose medium containing SCF, GM-CSF, IL-3, and erythropoietin (StemCell Technologies). Pen/Strep was added into the Methocult. The culture dishes were incubated in a humidified incubator at 37° C. Colonies containing at least 30 cells were counted at day 14 post-plating using StemVision (StemCell Technologies) to take the image of entire plate. The total number of colonies, number of CFU-GEMM (Granulocyte, Erythrocyte, Macrophage, Megakaryocyte), CFU-GM (Granulocyte, Macrophage), CFU-M (Macrophage), CFU-E (erythroid) and BFU-E (Burst-forming unit-erythroid) were then counted StemVision image analyzer software and confirmed by manually using StemVision Colony Marker software.

In vivo engraftment study. In vivo engraftment studies are conducted under protocol approved by IACUC. A fraction of final culture of genome edited HSC equivalent to 30,000 starting cells are injected intravenously via the tail vein into sub-lethally irradiated (200 cGY) 6- to 8-week old NSG mice. Engraftment is performed within 24 h after irradiation. Engraftment is monitored by flow cytometric analysis of blood collected at 4, 8, and 12 weeks post-infusion using anti-human CD45 and anti-mouse CD45 antibodies. The mice are sacrificed 13 weeks post-transplantation and bone marrow, spleen and thymus collected for analysis by flow cytometry and colony forming cell unit assay. For secondary engraftment, 50% of the bone marrow from each recipient mouse is transplanted into one secondary sub-lethally irradiated NSG mouse. Engraftment is monitored by flow cytometric analysis of blood collected at 4, 8, and 12 weeks post-infusion using panleukocyte marker, CD45 using anti-human CD45 and anti-mouse CD45 antibodies. Fifteen weeks after transplantation, bone marrow and spleen were harvested from the secondary mice and analyzed by flow cytometry and colony forming cell unit assay.

Results:

Without being bound by theory, it is believed that targeted genetic disruption of BCL11A erythroid enhancer in HSC will down regulate the expression of BCL11A selectively in erythroid cell lineage and relieve repression of γ-globin expression, allowing production of the red blood cells containing elevated HbF protein, F-cells. The elevated HbF prevents sickling of the red blood cells under deoxygenated conditions and will be therapeutic/curative for the patients of both β-thalassemia and SCD. Autologous hematopoietic stem cell transplantation (HSCT) with ex vivo genome edited HSC from SCD patients was also combined with stem cell expansion enhancing technology, e.g., an aryl hydrocarbon receptor (AHR) inhibitor, e.g., as described in WO2010/059401 (the contents of which are incorporated by reference in their entirety), e.g., Compound 4 to improve ex vivo expansion and increase the dose of gene modified HSC delivered.

For efficient genome editing via programmable nuclease, Cas9, the successful delivery of guide RNA (gRNA) and Cas9 protein into target cells and tissues is essential. Recent reports demonstrated that Cas9 ribonucleoprotein (RNP) complexes when delivered into target cells by electroporation can accomplish efficient and specific genome editing in several different cell types. Cas9-RNP complexes cleave chromosomal DNA almost immediately after delivery and are degraded rapidly in cells, reducing off-target effects. In contrast, use of plasmid and viral vector systems used to deliver Cas9 results in prolonged expression of the enzyme aggravating off-target effects associated with the system. Additionally, delivery of RNPs into the target cells requires no additional tools which would greatly facilitate translation of genome editing for therapeutic purposes in the clinic. Purified recombinant Cas9 protein and gRNA complexes (RNPs) were delivered into cultured HSPC and an overview experiments used are shown in FIG. 17.

Recombinant Cas9 protein was purified from Escherichia coli and complexed with synthetic dual gRNAs (dgRNA) that consist of crRNA and tracr or full-length single guide RNA (sgRNA) to generate ribonucleoprotein (RNP) complexes. The list and sequences of gRNAs used in the study are shown in Table 14. The RNP complexes were electroporated into healthy or SCD patient derived bone marrow CD34+ HSPC via electroporation as described under materials and methods. The cells were expanded for 2-days in HSC expansion medium containing Compound 4 prior to the delivery of RNP complexes. Actively dividing cells may facilitate uptake of RNP complexes delivered by electroporation. To facilitate recovery from transfection process, the cells were cultured for two additional days in the modified expansion medium containing compound 4. Viability of the cells 48 hours after electroporation was determined by flow cytometry using 7AAD. The viability was relatively high with >80% of the cells viable (FIG. 18) suggesting that the HSPC tolerated electroporation of the RNP complexes relatively well compared to other methods of Cas9 and gRNA delivery systems reported in the literature.

TABLE 14 List of gRNAs targeting BCL11A erythroid specific enhancer used in the current study. Guide RNA targeting Region/ dgRNA sgRNA domain ID strand tested tested Target Sequence Coordinates (hg38) CR000245 +58/+ x tcagtgagatgagatatcaa chr2: 60494483-60494502 CR000246 +58/+ x cagtgagatgagatatcaaa chr2: 60494484-60494503 CR000260 +58/− x tgtaactaataaataccagg chr2: 60494790-60494809 CR001124 +58/− x ttagggtgggggcgtgggtg chr2: 60495217-60495236 CR001131 +58/− x attagggtgggggcgtgggt chr2: 60495218-60495237 CR000309 +58/+ x X cacgcccccaccctaatcag chr2: 60495221-60495240 CR000308 +58/− x X tctgattagggtgggggcgt chr2: 60495222-60495241 CR000310 +58/− x X ttggcctctgattagggtgg chr2: 60495228-60495247 CR000311 +58/− x X tttggcctctgattagggtg chr2: 60495229-60495248 CR000312 +58/− x X gtttggcctctgattagggt chr2: 60495230-60495249 CR000313 +58/− x X ggtttggcctctgattaggg chr2: 60495231-60495250 CR000314 +58/− x X aagggtttggcctctgatta chr2: 60495234-60495253 CR000315 +58/− x X gaagggtttggcctctgatt chr2: 60495235-60495254 CR001128/ +58/+ X atcagaggccaaacccttcc chr2: 60495236-60495255 sgEH15 CR001127/ +58/− X cacaggctccaggaagggtt chr2: 60495247-60495266 sgEH14 CR001126/ +58/− x X tttatcacaggctccaggaa chr2: 60495252-60495271 sgEH13 CR001125/ +58/− X ttttatcacaggctccagga chr2: 60495253-60495272 sgEH12 CR000316/ +58/− X ttgcttttatcacaggctcc chr2: 60495257-60495276 sgEH11 CR000317/ +58/− ctaacagttgcttttatcac chr2: 60495264-60495283 sgEH4

The T7E1 assay is a convenient method to assess editing at specific sites in the genome. The genomic DNA was extracted from the HSPC 2-days post-electroporation. The targeted BCL11A erythroid enhancer region was amplified by polymerase chain reaction (PCR). The PCR products were subjected to T7E1 assay. The end products of T7E1 assay were subjected to 2% agarose gel electrophoresis and the percent edited alleles quantified by imageJ (http://rsb.info.nih.gov/ij/). Expected PCR product sizes and approximate expected sizes of T7E1-digested fragments are shown in FIG. 19. The total editing frequencies are indicated as percentage of total edits below the agarose gel image. The genome editing at the BCL11A locus was observed in the cells treated with BCL11A Cas9 RNPs but not in mock electroporated control cells (FIG. 19).

The genomic PCR products of the +58 erythroid enhancer region of BCL11A were also subjected to next generation sequencing (NGS). The NGS facilitates simultaneous monitoring of a large number of samples giving a global view of the alleles. Moreover, it provides information on the heterogeneity of insertions and deletions (indels). The sequences were compared with the sequences from control (mock) treated cells. The results of sequence analysis showed that CRISPR-Cas9 induced double stranded breaks were repaired by NHEJ resulting in variable frequencies of small deletions and insertions (indels) near Cas9 cleavage site located in +58 BCL11A erythroid enhancer region (FIG. 20 and Table 15). Overall, the observed editing efficiencies was higher for sgRNAs compared to dgRNAs targeting the same sequence, with 12 out 14 sgRNA producing editing at more than 50% alleles (FIG. 20 and Table 15), though (without being bound by theory) the differences in efficiency between sgRNA and dgRNA may be affected by the source of the materials.

TABLE 15 Genotypes identified by NGS in HSPCs edited with Cas9-RNP. The nucleotide sequence for each population is given. The target sequence targeted by each gRNA is indicated above each indel population, with the PAM sequences indicated in lower case. Dashes denote deleted bases and lowercase letters denote insertions. In the description of the gRNA, dgRNA refers to dual gRNA molecules comprising the indicated targeting domain sgRNA indicates single gRNA molecules comprising the indicated targeting domain. Where multiple experiments were run with the same dgRNA or sgRNA, successive experiments are labeled “dgRNA,” “d1gRNA”, “d2gRNA,” etc. % Indel gRNA Variant Allele length CTAACAGTTGCTTTTATCACagg CR00317- TAGTGCAAGCTAACAG---------------GCTCCAGGAAGGGTTTGGCCTCTGATTAG 5.96% −15 dgRNA CR00317- TAGTGCAAGCTAACAGTTGCTTTTATtCACAGGCTCCAGGAAGGGTTTGGCCTCTGATTAG 5.77% 1 dgRNA CR00317- TAGTGCAAGCTAACAGTTGCT-------------CCAGGAAGGGTTTGGCCTCTGATTAG 4.69% −13 dgRNA CR00317- TAGTGCAAGCTAACAGTTGCTTTTATCA--GGCTCCAGGAAGGGTTTGGCCTCTGATTAG 0.90% −2 dgRNA CR00317- TAGTGCAAGCTAACAGTTGCTTTTA-CACAGGCTCCAGGAAGGGTTTGGCCTCTGATTAG 0.88% −1 dgRNA CR00317- TAGTGCAAGCTAACAGTTGCTTTT--CACAGGCTCCAGGAAGGGTTTGGCCTCTGATTAG 0.77% −2 dgRNA CR00317- TAGTGCAAGCT-----------------------CCAGGAAGGGTTTGGCCTCTGATTAG 0.67% −23 dgRNA ATCAGAGGCCAAACCCTTCCacc CR001128- AGCTAACAGTTGCTTTTATCACAGGCTCCAGGA-GGGTTTGGCCTCTGATTAGGGTGGGG 20.07% −1 dgRNA CR001128- AGCTAACAGTTGCTTTTATCACAGGCTCCAGG-----TTTGGCCTCTGATTAGGGTGGGG 5.00% −5 dgRNA CR001128- AGCTAACAGTTGCTTTTATCACAGGCTCCAGGAAaGGGTTTGGCCTCTGATTAGGGTGGGG 4.84% 1 dgRNA CR001128- AGCTAACAGTTGCTTTTATCACAGGCTCCAGG----GTTTGGCCTCTGATTAGGGTGGGG 4.01% −4 dgRNA CR001128- AGCTAACAGTTGCTTTTATCACAGGCTCCAGGA--GGTTTGGCCTCTGATTAGGGTGGGG 2.99% −2 dgRNA CR001128- AGCTAACAGTTGCTTTTATCACAGGCTCCAGGA-GGGTTTGGCCTCTGATTAGGGTGGGG 23.33% −1 sgRNA CR001128- AGCTAACAGTTGCTTTTATCACAGGCTCCAGGAAGG-TTTGGCCTCTGATTAGGGTGGGG 5.77% −1 sgRNA CR001128- AGCTAACAGTTGCTTTTATCACAGGCTCCAGGAAaGGGTTTGGCCTCTGATTAGGGTGGGG 5.77% 1 sgRNA CR001128- AGCTAACAGTTGCTTTTATCACAGGCTCCAGGA--GGTTTGGCCTCTGATTAGGGTGGGG 5.37% −2 sgRNA CR001128- AGCTAACAGTTGCTTTTATCACAGGCTCCAGGAAG--TTTGGCCTCTGATTAGGGTGGGG 3.70% −2 sgRNA CR001128- AGCTAACAGTTGCTTTTATCACAGGCTCCAGG----------CCTCTGATTAGGGTGGGG 3.62% −10 sgRNA CR001128- AGCTAACAGTTGCTTTTATCACAGGC-----------------CTCTGATTAGGGTGGGG 3.54% −17 sgRNA CR001128- AGCTAACAGTTGCTTTTATCACAGGCTCCAGGA---GTTTGGCCTCTGATTAGGGTGGGG 2.97% −3 sgRNA TTGCTTTTATCACAGGCTCCagg CR00316- AGCTAACAGTTGCTTTTATCACAGG-------AAGGGTTTGGCCTCTGATTAGGGTGGGG 16.03% −7 sgRNA CR00316- AGCTAACAGTTGCTTTTATCACAGGCTtCCAGGAAGGGTTTGGCCTCTGATTAGGGTGGGG 8.25% 1 sgRNA CR00316- AGCTAACAGTTGCTTTTATC--------CAGGAAGGGTTTGGCCTCTGATTAGGGTGGGG 8.04% −8 sgRNA CR00316- AGCTAACAGTTGCTTTTATCACAGGCcTCCAGGAAGGGTTTGGCCTCTGATTAGGGTGGGG 4.07% 1 sgRNA CR00316- AGCTAACAGTTGCTTTTATCACAGGC-CCAGGAAGGGTTTGGCCTCTGATTAGGGTGGGG 3.55% −1 sgRNA CR00316- AGCTAACAGTTGCTTTTATCACAGGC--CAGGAAGGGTTTGGCCTCTGATTAGGGTGGGG 2.37% −2 sgRNA CR00316- AGCTAACAGTTGCTTTTATCACAGG-------AAGGGTTTGGCCTCTGATTAGGGTGGGG 2.49% −7 dgRNA CR00316- AGCTAACAGTTGCTTTTATCACAGGCTtCCAGGAAGGGTTTGGCCTCTGATTAGGGTGGGG 1.78% 1 dgRNA CR00316- AGCTAACAGTTGCTTTTATC--------CAGGAAGGGTTTGGCCTCTGATTAGGGTGGGG 1.32% −8 dgRNA CR00316- AGCTAACAGTTGCTTTTATCACAGGCcTCCAGGAAGGGTTTGGCCTCTGATTAGGGTGGGG 1.26% 1 dgRNA CR00316- AGCTAACAGTTGCTTTTATCACAGG-------AAGGGTTTGGCCTCTGATTAGGGTGGGG 6.94% −7 d1gRNA CR00316- AGCTAACAGTTGCTTTTATC--------CAGGAAGGGTTTGGCCTCTGATTAGGGTGGGG 4.99% −8 d1gRNA CR00316- AGCTAACAGTTGCTTTTATCACAGGCTtCCAGGAAGGGTTTGGCCTCTGATTAGGGTGGGG 4.69% 1 d1gRNA CR00316- AGCTAACAGT-------------------------------------GATTAGGGTGGGG 2.90% −37 d1gRNA CR00316- AGCTAACAGTTGCTTTTATCACAGGC-CCAGGAAGGGTTTGGCCTCTGATTAGGGTGGGG 1.54% −1 d1gRNA CR00316- AGCTAACAGTTGCTTTTATCACAGG-------AAGGGTTTGGCCTCTGATTAGGGTGGGG 11.64% −7 d2gRNA CR00316- AGCTAACAGTTGCTTTTATC--------CAGGAAGGGTTTGGCCTCTGATTAGGGTGGGG 6.04% −8 d2gRNA CR00316- AGCTAACAGTTGCTTTTATCACAGGCTtCCAGGAAGGGTTTGGCCTCTGATTAGGGTGGGG 5.40% 1 d2gRNA CR00316- AGCTAACAGTTGCTTTTATCACAGGCcTCCAGGAAGGGTTTGGCCTCTGATTAGGGTGGGG 1.80% 1 d2gRNA CR00316- AGCTAACAGTTGCTTTTATCACAGGC-----GAAGGGTTTGGCCTCTGATTAGGGTGGGG 1.43% −5 d2gRNA TTTTATCACAGGCTCCAGGAagg CR001125- AACAGTTGCTTTTATCACAGGCTCCAaGGAAGGGTTTGGCCTCTGATTAGGGTGGGGGCGT 13.50% 1 dgRNA CR001125- AACAGTTGCTTTTATCACAGGC-----------------CTCTGATTAGGGTGGGGGCGT 1.82% −17 dgRNA CR001125- AACAGTTGCTTTTATCACAGG-----------GTTTGGCCTCTGATTAGGGTGGGGGCGT 1.76% −11 dgRNA CR001125- AACAGTTGCTTTTATCACAGG-------AAGGGTTTGGCCTCTGATTAGGGTGGGGGCGT 1.59% −7 dgRNA CR001125- AACAGTTGCTTTT------------------------------------GGTGGGGGCGT 1.33% −36 dgRNA CR001125- AACAGTTGCTTTTATCACAGGCTCCAaGGAAGGGTTTGGCCTCTGATTAGGGTGGGGGCGT 26.27% 1 sgRNA CR001125- AACAGTTGCTTTTATCACAGG-----------GTTTGGCCTCTGATTAGGGTGGGGGCGT 4.64% −11 sgRNA CR001125- AACAGTTGCTTTTATCACAGG-------AAGGGTTTGGCCTCTGATTAGGGTGGGGGCGT 4.11% −7 sgRNA CR001125- AACAGTTGCTTTTATCACAGGC-----------------CTCTGATTAGGGTGGGGGCGT 2.66% −17 sgRNA CR001125- AACAGTTGCTTTTATCACAGGCT------------TGGCCTCTGATTAGGGTGGGGGCGT 2.58% −12 sgRNA CR001125- AACAGTTGCTTTTATCACAGGCTCC-GGAAGGGTTTGGCCTCTGATTAGGGTGGGGGCGT 1.84% −1 sgRNA TTTATCACAGGCTCCAGGAAggg CR001126- ACAGTTGCTTTTATCACAGGCTCCAG-AAGGGTTTGGCCTCTGATTAGGGTGGGGGCGTG 9.38% −1 dgRNA CR001126- ACAGTTGCTTTTATCACAGG-----------GTTTGGCCTCTGATTAGGGTGGGGGCGTG 3.28% −11 dgRNA CR001126- ACAGTTGCTTTTATCACAGGCTCCAGGgAAGGGTTTGGCCTCTGATTAGGGTGGGGGCGTG 2.91% 1 dgRNA CR001126- ACAGTTGCTTTTATCACAGGC-----------------CTCTGATTAGGGTGGGGGCGTG 2.82% −17 dgRNA CR001126- ACAGTTGCTTTT---------------------------------------GGGGGCGTG 1.61% −39 dgRNA CR001126- ACAGTTGCTTT----------------------------------------GGGGGCGTG 1.12% −40 dgRNA CR001126- ACAGTTGCTTTTATCACAGGCTCCAG-AAGGGTTTGGCCTCTGATTAGGGTGGGGGCGTG 12.70% −1 sgRNA CR001126- ACAGTTGCTTTTATCACAGG-----------GTTTGGCCTCTGATTAGGGTGGGGGCGTG 4.37% −11 sgRNA CR001126- ACAGTTGCTTTTATCACAGGCTCCAGGgAAGGGTTTGGCCTCTGATTAGGGTGGGGGCGTG 3.22% 1 sgRNA CR001126- ACAGTTGCTTTTATCACAGGCTCCAGaT------------------AAGGTGGGGGCGTG 2.96% −18 sgRNA CR001126- ACAGTTGCTTTTATCACAGGC-----------------CTCTGATTAGGGTGGGGGCGTG 2.68% −17 sgRNA CR001126- ACAGTTGCTTTTATCACAGGCTCCAGG----GTTTGGCCTCTGATTAGGGTGGGGGCGTG 2.59% −4 sgRNA CR001126- ACAGTTGCTTTTATCACAGGCTCCAGcGAAGGGTTTGGCCTCTGATTAGGGTGGGGGCGTG 1.80% 1 sgRNA CR001126- ACAGTTGCTTTTATCACAGGCTCC-GGAAGGGTTTGGCCTCTGATTAGGGTGGGGGCGTG 1.74% −1 sgRNA CACAGGCTCCAGGAAGGGTTtgg CR001127- TGCTTTTATCACAGGCTCCAGGAAGG-TTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGG 4.00% −1 dgRNA CR001127- TGCTTTTATCACAGGCcT-----------------------------GGGGCGTGGGTGG 2.35% −29 dgRNA CR001127- TGCTTTTATCACAGGC------------------------------------GTGGGTGG 2.19% −36 dgRNA CR001127- TGCTTTTATCACAGGC-----------------CTCTGATTAGGGTGGGGGCGTGGGTGG 1.59% −17 dgRNA CR001127- TGCTTTTATCACAGGCTCCAGGAAGG------CCTCTGATTAGGGTGGGGGCGTGGGTGG 1.48% −6 dgRNA CR001127- TGCTTTTATCACAGGCTCCAGGA-GGGTTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGG 23.21% −1 sgRNA CR001127- TGCTTTTATCACAGGCTCCAGGAAGG-TTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGG 6.65% −1 sgRNA CR001127- TGCTTTTATCACAGGC-----------------CTCTGATTAGGGTGGGGGCGTGGGTGG 5.20% −17 sgRNA CR001127- TGCTTTTATCACAGGCTCCAGGAAaGGGTTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGG 4.89% 1 sgRNA CR001127- TGCTTTTATCACAGGCTCCAGG----------------------------GCGTGGGTGG 4.30% −28 sgRNA CR001127- TGCTTTTATCACAGGCTCCAGG-----TTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGG 3.72% −5 sgRNA CR001127- TGCTTTTATCACAGGC------------------------------------GTGGGTGG 3.71% −36 sgRNA CR001127- TGCTTTTATCACAGGCTCCAGGAAG--TTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGG 3.53% −2 sgRNA CR001127- TGCTTTTATCACAGGCTCCAGGAAGGtC-----------------CGTTTGCGTGGGTGG 2.29% −17 sgRNA CACGCCCCCACCCTAATCAGagg CR00309- TATCACAGGCTCCAGGAAGGGTTTGGC-------------------GTGGGTGGGGTAGA 11.56% −19 sgRNA CR00309- TATCACAGGCTCCAGGAAGGGTTTGGCCTCTGAaTTAGGGTGGGGGCGTGGGTGGGGTAGA 7.29% 1 sgRNA CR00309- TATCACAGGCTCCAGGAAGGG------------------------CGTGGGTGGGGTAGA 6.16% −24 sgRNA CR00309- TATCACAGGCTCCAGGAAGGG----------------------GGCGTGGGTGGGGTAGA 4.74% −22 sgRNA CR00309- TATCACAGGCTCCAGGAAGGGTTTGG------------------GCGTGGGTGGGGTAGA 4.34% −18 sgRNA CR00309- TATCACAGGCTCCAGGAAGGGTTTGG------------------------GTGGGGTAGA 3.45% −24 sgRNA CR00309- TATCACAGGCTCCAGG---------------------------GGCGTGGGTGGGGTAGA 1.87% −27 sgRNA GAAGGGTTTGGCCTCTGATTagg CR00313- TCCAGGAAGGGTTTGG------------------------GTGGGGTAGAAGAGGACTGG 3.36% −24 sgRNA CR00313- TCCAGGAAGGGTTTGGCCTCTGATTAGG-TGGGGGCGTGGGTGGGGTAGAAGAGGACTGG 3.31% −1 sgRNA CR00313- TCCAGGAAGGGTT-----------------------------GGGGTAGAAGAGGACTGG 2.83% −29 sgRNA CR00313- TCCAGGAAGGGTTTGGCCT-------------------GGGTGGGGTAGAAGAGGACTGG 2.76% −19 sgRNA CR00313- TCCAGGAAGGGTTTGG------------------------------TAGAAGAGGACTGG 2.31% −30 sgRNA GTTTGGCCTCTGATTAGGGTggg CR00312- CCAGGAAGGGTTTGGCCTCTGATTAGG-TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGC 16.87% −1 dgRNA CR00312- CCAGGAAGGGTTTGGC-------------------GTGGGTGGGGTAGAAGAGGACTGGC 9.86% −19 dgRNA CR00312- CCAGGAAGGGTTTGGCCTCTGATT--GGTGGGGGCGTGGGTGGGGTAGAAGAGGACTGGC 5.65% −2 dgRNA CR00312- CCAGGAAGGG------------------------CGTGGGTGGGGTAGAAGAGGACTGGC 3.83% −24 dgRNA CR00312- CCAGGAAGGG----------------------GGCGTGGGTGGGGTAGAAGAGGACTGGC 3.42% −22 dgRNA CR00312- CCAGGAAGGGTTTGG------------------------GTGGGGTAGAAGAGGACTGGC 2.10% −24 dgRNA CR00312- CCAGGAAGGGTTTGGCCTCTGA----GGTGGGGGCGTGGGTGGGGTAGAAGAGGACTGGC 1.85% −4 dgRNA CR00312- CCAGGAAGGGTTTGGCCTCTGATTAGG-TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGC 13.35% −1 sgRNA CR00312- CCAGGAAGGGTTTGGC-------------------GTGGGTGGGGTAGAAGAGGACTGGC 7.85% −19 sgRNA CR00312- CCAGGAAGGGTTTGG------------------------GTGGGGTAGAAGAGGACTGGC 4.19% −24 sgRNA CR00312- CCAGGAAGGGTTTGGCCTCTGATT--GGTGGGGGCGTGGGTGGGGTAGAAGAGGACTGGC 3.98% −2 sgRNA CR00312- CCAGGAAGGGTTTGGCCTCTGATTAGGG-----GCGTGGGTGGGGTAGAAGAGGACTGGC 2.95% −5 sgRNA CR00312- CCAGGAAGGG------------------------CGTGGGTGGGGTAGAAGAGGACTGGC 2.29% −24 sgRNA CR00312- CCAGGAAGGGTTTGGCCTCTGATTAGaGGTGGGGGCGTGGGTGGGGTAGAAGAGGACTGGC 2.09% 1 sgRNA CR00312- CCAGGAAGGGTTTGGCCTCTGATTAGG-TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGC 19.22% −1 d1gRNA CR00312- CCAGGAAGGGTTTGGCCTCTGATT--GGTGGGGGCGTGGGTGGGGTAGAAGAGGACTGGC 6.28% −2 d1gRNA CR00312- CCAGGAAGGGTTTGG------------------------GTGGGGTAGAAGAGGACTGGC 5.31% −24 d1gRNA CR00312- CCAGGAAGGGTTTGGC-------------------GTGGGTGGGGTAGAAGAGGACTGGC 4.22% −19 d1gRNA CR00312- CCAGGAAGGGTTTGG----------------GGGCGTGGGTGGGGTAGAAGAGGACTGGC 3.10% −16 d1gRNA CR00312- CCAGGAAGGGTTTGGCCTCTGATTAG--TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGC 2.85% −2 d1gRNA CR00312- CCAGGAAGGG------------------------CGTGGGTGGGGTAGAAGAGGACTGGC 2.74% −24 d1gRNA CR00312- CCAGGAAGGGTTTGGCCTCTGATTAGG-TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGC 23.15% −1 d2gRNA CR00312- CCAGGAAGGGTTTGGC-------------------GTGGGTGGGGTAGAAGAGGACTGGC 8.99% −19 d2gRNA CR00312- CCAGGAAGGGTTTGGCCTCTGATT--GGTGGGGGCGTGGGTGGGGTAGAAGAGGACTGGC 6.82% −2 d2gRNA CR00312- CCAGGAAGGG-----------------------GCGTGGGTGGGGTAGAAGAGGACTGGC 2.69% −23 d2gRNA CR00312- CCAGGAAGGG------------------------CGTGGGTGGGGTAGAAGAGGACTGGC 2.29% −24 d2gRNA CR00312- CCAGGAAGGGTTTGGCCTCTGATTAG--TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGC 2.25% −2 d2gRNA CR00312- CCAGGAAGGGTTTGG----------------GGGCGTGGGTGGGGTAGAAGAGGACTGGC 2.13% −16 d2gRNA TTTGGCCTCTGATTAGGGTGggg CR00311- CAGGAAGGGTTTGGCCTCTGATTAGG-TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCA 19.62% −1 dgRNA CR00311- CAGGAAGGGTTTGGC-------------------GTGGGTGGGGTAGAAGAGGACTGGCA 3.01% −19 dgRNA CR00311- CAGGAAGGGTTTGGCCTCTGATTAG--TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCA 2.77% −2 dgRNA CR00311- CAGGAAGGGTTTGGCCTCTGATTAGGG-----GCGTGGGTGGGGTAGAAGAGGACTGGCA 2.23% −5 dgRNA CR00311- CAGGAAGGGTTTGG------------------------GTGGGGTAGAAGAGGACTGGCA 2.21% −24 dgRNA CR00311- CAGGAAGGGTTTGG-------------TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCA 2.05% −13 dgRNA CR00311- CAGGAAGGGTTTGGCCTCTG-------TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCA 1.88% −7 dgRNA CR00311- CAGGAAGGGT------------------------------GGGGTAGAAGAGGACTGGCA 1.76% −30 dgRNA CR00311- CAGGAAGGGTTTGGCCTCTGATTAGG-TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCA 28.21% −1 sgRNA CR00311- CAGGAAGGGTTTGGC-------------------GTGGGTGGGGTAGAAGAGGACTGGCA 4.88% −19 sgRNA CR00311- CAGGAAGGGT------------------------------GGGGTAGAAGAGGACTGGCA 2.72% −30 sgRNA CR00311- CAGGAAGGGTTTGGCCTCTGATTAG--TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCA 2.62% −2 sgRNA CR00311- CAGGAAGGGTTTGGCCTCTGATTAGGG----GGCGTGGGTGGGGTAGAAGAGGACTGGCA 2.35% −4 sgRNA CR00311- CAGGAAGGGTTTGGCCTCTGATTAGGG-----GCGTGGGTGGGGTAGAAGAGGACTGGCA 2.06% −5 sgRNA CR00311- CAGGAAGGGTTTGGCCTCTGATTAGG-TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCA 31.34% −1 d1gRNA CR00311- CAGGAAGGGTTTGGCCTCTGATTAG--TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCA 4.00% −2 d1gRNA CR00311- CAGGAAGGGTTTGGCCT------------------------------AAGAGGACTGGCA 2.84% −30 d1gRNA CR00311- CAGGAAGGGTTTGG-----------------------------------GAGGACTGGCA 2.41% −35 d1gRNA CR00311- CAGGAAGGGTTT---------------------------------AGAAGAGGACTGGCA 2.35% −33 d1gRNA CR00311- CAGGAAGGGTTTGGCCTC-------------------------------GAGGACTGGCA 2.11% −31 d1gRNA CR00311- CAGGAAGGGTTTGGCCTCTGATTAGGG----GGCGTGGGTGGGGTAGAAGAGGACTGGCA 2.03% −4 d1gRNA CR00311- CAGGAAGGGTTTGGCCTCTGATTAGGG---GGGCGTGGGTGGGGTAGAAGAGGACTGGCA 1.71% −3 d1gRNA CR00311- CAGGAAGGGTTTGGCCTCTGATTAGG-TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCA 30.20% −1 d2gRNA CR00311- CAGGAAGGGTTTGGC-------------------GTGGGTGGGGTAGAAGAGGACTGGCA 7.57% −19 d2gRNA CR00311- CAGGAAGGGTTTGGCCTCTGATTAG--TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCA 3.57% −2 d2gRNA CR00311- CAGGAAGGGTTTGG----------------------------GGTAGAAGAGGACTGGCA 2.39% −28 d2gRNA CR00311- CAGGAAGGGTTTGGCCTCTGATTAGGG-----GCGTGGGTGGGGTAGAAGAGGACTGGCA 2.10% −5 d2gRNA CR00311- CAGGAAGGGTTTGGCCTCTGATTAGGG----GGCGTGGGTGGGGTAGAAGAGGACTGGCA 1.50% −4 d2gRNA CR00311- CAGGAAGGGTTTGG----------------GGGCGTGGGTGGGGTAGAAGAGGACTGGCA 1.49% −16 d2gRNA TTGGCCTCTGATTAGGGTGGggg CR00310- AGGAAGGGTTTGGCCTCTGATTAGGG----GGCGTGGGTGGGGTAGAAGAGGACTGGCAG 7.70% −4 sgRNA CR00310- AGGAAGGGTTTGGCCTCTGATTAGGG------CGTGGGTGGGGTAGAAGAGGACTGGCAG 7.13% −6 sgRNA CR00310- AGGAAGGGTTTGGCCTCTGATTAGGG-----GCGTGGGTGGGGTAGAAGAGGACTGGCAG 6.34% −5 sgRNA CR00310- AGGAAGGGTTTGGCCTCTGATTAGG-TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCAG 5.38% −1 sgRNA CR00310- AGGAAGGGTTTGGCCTCTGATTAG--TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCAG 3.73% −2 sgRNA CR00310- AGGAAGGGTTTGGCCTCTGATT-----GGGGGCGTGGGTGGGGTAGAAGAGGACTGGCAG 3.54% −5 sgRNA CR00310- AGGAAGGGTTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGGG-TAGAAGAGGACTGGCAG 0.67% −1 dgRNA TCTGATTAGGGTGGGGGCGTggg CR00308- GGTTTGGCCTCTGATTAGGGTGGGG------------TAGAAGAGGACTGGCAGACCTCT 16.28% −12 sgRNA CR00308- GGTTTGGCCTCTGATTAGGGTGGGGG-----------TAGAAGAGGACTGGCAGACCTCT 5.59% −11 sgRNA CR00308- GGTTTGGCCTCTGATTAGGGTGGG--------TGGGGTAGAAGAGGACTGGCAGACCTCT 4.51% −8 sgRNA CR00308- GGTTTGGCCTCTGAT------------------GGGGTAGAAGAGGACTGGCAGACCTCT 3.54% −18 sgRNA CR00308- GGTTTGGCCTCTGATTtA-----------------------------CTGGCAGACCTCT 2.76% −29 sgRNA CR00308- GGTTTGGCCTCTGATTgG-------CCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTCT 2.27% −7 sgRNA CR00308- GGTTTGGCCTCTGATTAGGG----------------GTAGAAGAGGACTGGCAGACCTCT 2.26% −16 sgRNA CR00308- GGTTTGGCCTCTGATcC--AAGAGCCCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTCT 1.99% −2 sgRNA CR00308- GGTTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGGG-TAGAAGAGGACTGGCAGACCTCT 0.42% −1 dgRNA ATTAGGGTGGGGGCGTGGGTggg CR001131- TGGCCTCTGATTAGGGTGGGG------------TAGAAGAGGACTGGCAGACCTCTCCAT 44.62% −12 dgRNA CR001131- TGGCCTCTGATTAGGGTGGGGG-----------TAGAAGAGGACTGGCAGACCTCTCCAT 3.19% −11 dgRNA CR001131- TGGCCTCTGATTAGGGTGGGGGCGTGG-TGGGGTAGAAGAGGACTGGCAGACCTCTCCAT 1.72% −1 dgRNA CR001131- TGGCCTCTGATTAGGGTGGGGGCG------------AAGAGGACTGGCAGACCTCTCCAT 1.04% −12 dgRNA TTAGGGTGGGGGCGTGGGTGggg CR001124- GGCCTCTGATTAGGGTGGGG------------TAGAAGAGGACTGGCAGACCTCTCCATC 8.52% −12 dgRNA CR001124- GGCCTCTGATTAGGGTGGGGGCGTGG-TGGGGTAGAAGAGGACTGGCAGACCTCTCCATC 2.12% −1 dgRNA CR001124- GGCCTCTGATTAGGGTGGGGG-----------TAGAAGAGGACTGGCAGACCTCTCCATC 1.33% −11 dgRNA TGTAACTAATAAATACCagg CR00260- CTGCTGAGGTGTAACTAATAAATACC-GGAGGCAGCATTTTAGTTCACAAGCTCGGAGCA 26.54% −1 dgRNA CR00260- CTGCTGAGGTGTAACTAATAAATAC-AGGAGGCAGCATTTTAGTTCACAAGCTCGGAGCA 12.39% −1 dgRNA CR00260- CTGCTGAGGTGTAACTAATAAATACCcAGGAGGCAGCATTTTAGTTCACAAGCTCGGAGCA 12.32% 1 dgRNA CR00260- CTGCTGAGGTGTAACTAATAAATACC--GAGGCAGCATTTTAGTTCACAAGCTCGGAGCA 2.37% −2 dgRNA CR00260- CTGCTGAGGTGTAACTAATAAAT--CAGGAGGCAGCATTTTAGTTCACAAGCTCGGAGCA 1.89% −2 dgRNA CR00260- CTGCTGAGGTGTAACTAATAAATA---GGAGGCAGCATTTTAGTTCACAAGCTCGGAGCA 1.28% −3 dgRNA CAGTGAGATGAGATATCAAAggg CR00246- GGGAGATGGAATGAACACTTTTCGTCCCCTTTGgATATCTCATCTCACTGAGCTCTGGGCC 7.56% 1 dgRNA CR00246- GGGAGATGGAATGAACACTTTTCGTCCCCTTTGAT--CTCATCTCACTGAGCTCTGGGCC 4.46% −2 dgRNA CR00246- GGGAGATGGAATGAACACTTTTCGTCCCCTTTG------CATCTCACTGAGCTCTGGGCC 3.50% −6 dgRNA CR00246- GGGAGATGGAATGAACACTTTTCGTCCCCTTT-----CTCATCTCACTGAGCTCTGGGCC 2.98% −5 dgRNA CR00246- GGGAGATGGAATGAACACTTTTCGTCCCCTTT-ATATCTCATCTCACTGAGCTCTGGGCC 2.97% −1 dgRNA CR00246- GGGAGATGGAATGAACACTTTTCGTCCCCTTTG---TCTCATCTCACTGAGCTCTGGGCC 2.96% −3 dgRNA CR00246- GGGAGATGGAATGAACACTTTTCGTCCCCTTT--TATCTCATCTCACTGAGCTCTGGGCC 2.93% −2 dgRNA CR00246- GGGAGATGGAATGAACACTTTTCGTCCCCTTTG-TATCTCATCTCACTGAGCTCTGGGCC 2.70% −1 dgRNA TCAGTGAGATGAGATATCAAagg CR00245- GGAGATGGAATGAACACTTTTCGTCCCCTTTGAaTATCTCATCTCACTGAGCTCTGGGCCG 22.36% 1 dgRNA CR00245- GGAGATGGAATGAACACTTTTCGTCCCCTTTGA-ATCTCATCTCACTGAGCTCTGGGCCG 8.97% −1 dgRNA CR00245- GGAGATGGAATGAACACTTTTCGTCCCCTTTGAT--CTCATCTCACTGAGCTCTGGGCCG 4.03% −2 dgRNA CR00245- GGAGATGGAATGAACACTTTTCGTCCCCTTTG-TATCTCATCTCACTGAGCTCTGGGCCG 2.45% −1 dgRNA CR00245- GGAGATGGAATGAACACTTTTCGTCCCCTT--ATATCTCATCTCACTGAGCTCTGGGCCG 1.85% −2 dgRNA CR00245- GGAGATGGAATGAACACTTTTCGTCCCCTTTGA-----CATCTCACTGAGCTCTGGGCCG 1.38% −5 dgRNA GTGCCAGATGAACTTCCCATtgg g7BCL11a-BC- CTGTGGGCAGTGCCAGATGAACTTCC-ATTGGGGGACATTCTTATTTTTATCGAGCACAA 15.63% −1 1sgRNA g7BCL11a-BC- CTGTGGGCAGTGCCAGATGAACTTC--ATTGGGGGACATTCTTATTTTTATCGAGCACAA 7.36% −2 1sgRNA g7BCL11a-BC- CTGTGGGCAGTGCCAGATGAACTTCCCcATTGGGGGACATTCTTATTTTTATCGAGCACAA 6.88% 1 1sgRNA g7BCL11a-BC- CTGTGGGCAGTGCCAGATGAAC-----ATTGGGGGACATTCTTATTTTTATCGAGCACAA 2.81% −5 1sgRNA g7BCL11a-BC- CTGTGGGCAGTGCCAGATGAACTTCC--TTGGGGGACATTCTTATTTTTATCGAGCACAA 2.59% −2 1sgRNA g7BCL11a-BC- CTGTGGGCAGTGCCAGATGAACTTCC-ATTGGGGGACATTCTTATTTTTATCGAGCACAA 18.89% −1 2sgRNA g7BCL11a-BC- CTGTGGGCAGTGCCAGATGAACTTC--ATTGGGGGACATTCTTATTTTTATCGAGCACAA 9.14% −2 2sgRNA g7BCL11a-BC- CTGTGGGCAGTGCCAGATGAACTTCCCcATTGGGGGACATTCTTATTTTTATCGAGCACAA 5.52% 1 2sgRNA g7BCL11a-BC- CTGTGGGCAGTGCCAGATGAACTTCC--TTGGGGGACATTCTTATTTTTATCGAGCACAA 4.39% −2 2sgRNA g7BCL11a-BC- CTGTGGGCAGTGCCAGATGAACT---CATTGGGGGACATTCTTATTTTTATCGAGCACAA 3.18% −3 2sgRNA

To determine whether CD34+ HSPC have retained their multilineage potential to differentiate into effector cells after ex vivo manipulations including genome editing, in vitro colony forming cell (CFC) unit assays were performed for select gRNAs. The genome edited cells were suspended in cytokine-supplemented methylcellulose and maintained for 14 days at 37° C. in a humidified atmosphere of 5% CO2. Discrete colonies developed which were classified and counted based on the number and types of mature cells using morphological and phenotypic criteria (STEMvision) that they contain and scored for contribution to colony forming unit-erythroid (CFU-E), burst forming unit-erythroid (BFU-E), colony-forming unit-granulocyte/macrophage (CFU-GM) and colony-forming unit-granulocyte/erythrocyte/macrophage/megakaryocyte (CFU-GEMM; FIG. 21). The colony forming potential of mock transfected cells was the highest followed by gRNAs targeting +58 erythroid enhancer of BCL11A. A similar number and types of colonies were observed for gRNAs targeting BCL11A erythroid enhancer. The guide RNA targeting exon 2 of BCL11A gave the least number of colonies (FIG. 22).

Relative mRNA expression levels of BCL11A, gamma- and beta-globin chains in unilineage erythroid cultures were quantified by Real-Time PCR. The transcript levels were normalized against human GAPDH transcript levels. The BCL11A mRNA levels were reduced in genome edited HSPC. In contrast, BCL11A mRNA levels remained the same in unedited or edited HSPC at the exon 2 of BCL11A on days 7 and 14 of erythroid differentiation (FIG. 23). Gamma globin mRNA levels increased and correspondingly beta-globin mRNA decreased gradually in edited HSPC during erythroid differentiation (FIG. 23). Increase in HbF and decrease in beta-globin (sickled globin) levels in erythrocytes derived from genome edited cells likely to have therapeutic implications by reduced sickling.

The genome edited and unedited HSPC at various stages (day 7, 14 and 21) of erythroid differentiation were analyzed by flow cytometry for expression levels of fetal globin and two erythroid cell surface markers, transferrin receptor (CD71) and glycophorin A (CD235a) using antibodies conjugated to fluorescent dyes. The live cells were identified and gated by exclusion of 7AAD. Genome editing did not adversely affect erythroid differentiation as the cultured cells showed similar levels of CD71 and CD235A positivity consistent with late stage erythroblasts. Genome editing of +58 erythroid enhancer region resulted in a larger increase in HbF containing cells (up to 67%) than other gRNAs and the mock electroporated cells (FIG. 24). Very high induction of HbF positive cells by g7 gRNA targeting exon 2 of BCL11A was observed. However, the cell proliferation and colony forming potential of exon 2 targeted cells was dramatically reduced (FIGS. 21 and 22).

Upon deep sequencing of the targeted region, we noticed that GATA1 and TAL1 binding motifs were intact in the genome edited target region (FIG. 25). Recent literature demonstrated the importance of GATA1 binding site in regulation of BCL11A expression and derepression of fetal globin. Viestra et al., Nature Methods. 2015, 12:927. In contrast to the literature reports, which showed the importance of the two motifs for maintenance of BCL11A levels in adult erythroid cells, our findings demonstrate that sequences upstream of the two transcription factor binding sites are also important in regulation of BCL11a gene expression, and genome editing exclusively at these upstream sites leads to upregulation of HbF, even when the GATA1 and TAL1 binding sites remain intact.

Example 3.1 Methods:

Human CD34⁺ cell culture. Human CD34+ cells were isolated from G-CSF mobilized peripheral blood from adult donors (AllCells) using immunoselection (Miltenyi) according to the manufacturer's instructions and expanded for 3 days using StemSpan SFEM (StemCell Technologies; Cat no. 09650) supplemented with 50 ng/mL each of thrombopoietin (Tpo), Flt3 ligand (Flt-3L, Life Technologies, Cat. #PHC9413), human stem cell factor (SCF, Life Technologies, Cat. #PHC2113) and human interleukin-6 (IL-6, Life Technologies, Cat. #PHC0063), as well as 1× antibiotic/antimycotic (Gibco, Cat. #10378-016) and 500 nM compound 4.

Assembly of Cas9 and guide RNA ribonucleoprotein (RNP) complexes, preparation of HSPC, and electroporation of RNP into HSPC. Cas9-guide RNA ribonucleoprotein complexes (RNPs) were prepared immediately prior to electroporation. For formation of RNP using dual guide RNAs (dgRNAs), 3 μg of each of crRNA (in 2.24 μL) and tracr (in 1.25 μL) are first denatured at 95° C. for 2 min in separate tubes and then cooled to room temperature. For preparation of Cas9 protein, 6 μg of CAS9 protein (in 1 μL) was mixed with 0.5 μL of 5×CCE buffer (20 mM HEPES, 100 mM KCL, 5 mM MgCL2, 5% Glycerol and freshly added 1 mM DTT). Tracr was first mixed with the Cas9 preparation and incubated at 37° C. for 5 min. The crRNA was then added to Tracr/CAS9 complexes and incubated for 5 min at 37° C. For the None/control condition, vehicle rather than crRNA was added to the Tracr/CAS9 complexes. The HSPC were collected by centrifugation and resuspended in P3 Primary Cell Solution (Lonza cat. No. PBP3-00675) at a cell density of 2.5×10⁶/mL. The RNP was mixed with 20 μL of cells by pipetting up and down and incubated at RT for 2 min. The RNP/cell mixture (20 μL) was electroporated using code CM-137 on the 4D-Nucleofector (Lonza). Duplicate 20 μL electroporations were performed. For the experiments in this Example 3.1, the tracr used was SEQ ID NO: 7808, and the crRNA had the following format and sequence, with 2′O-Methyl (m) and Phosphorothioate Bond (*) modifications indicated: mN*mN*mN*rNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrGrUrUrUrUrArGrArGrCrUrArU*mG*m C*mU, where N's are the nucleotides of the indicated targeting domain (e.g., as indicated by the CRxxxxx identifier).

In vitro erythropoiesis and FACS analysis for HbF containing erythroid cells. After electroporation, the cells were immediately transferred into 250 μL pre-warmed erythroid differentiation medium (EDM) consisting of IMDM (Hyclone, Cat. #SH30228.01), 330 μg/mL human holo-transferrin (Invitria Cat#777TRF029), 10 μg/mL recombinant human insulin (Gibco Cat#A1138211), 2 IU/mL heparin (Sigma, part #H3393), 5% human AB serum (Sigma, Cat# H4522), 125 ng/mL human erythropoietin (Peprotech #10779-058), and 1× antibiotic/antimycotic (Gibco, Cat. #10378-016). EDM was further supplemented with 1 μM hydrocortisone (Sigma H8672), 100 ng/mL human SCF (Life Technologies, Cat. #PHC2113), and 5 ng/mL human IL-3 (Peprotech #10779-598). After 2 days, the cell culture was diluted in fresh medium. Cultures were maintained for a total of 7 days, at which time the cells were analyzed by intracellular staining for HbF expression. Briefly, the cells were washed once with PBS, resuspended in LIVE/DEAD® Fixable Violet Dead Cell Stain (ThermoFisher L34963; 1:1000 in PBS) and incubated for 30 min. Cell were then washed and stained with anti-CD71-BV711 (Fisher Scientific Company Llc. BDB563767) and anti-CD235a-APC (BD 551336) antibodies for 30 min. The cells were then washed, followed by fixation with fixation buffer (Biolegend, Cat#420801) and permeabilized with 1× intracellular staining permeabilization wash buffer (Biolegend, Cat#421002) according to the manufacturer's instructions. The cells were then incubated with 0.5 μL of anti-HbF-PE antibody (Life Technologies, part #MHFH04) in 50 μL of 1× intracellular staining perm wash buffer for 20 min at room temperature. The cells were washed twice with 2 mL of 1× intracellular staining Perm wash buffer and resuspend in staining buffer and analyzed on an LSRFortessa flow cytometer (BD Biosciences) for HbF expression. The results were analyzed using Flowjo and data were presented as % of HbF positive cells (F-cells) in the viable CD71 positive erythroid cell population.

Genomic DNA preparation and next generation sequencing (NGS). Genomic DNA was prepared from edited and unedited HSPC at 48 hours post-electroporation using Quick Extract DNA Extraction Solution (Epicentre Cat # QE09050). To determine editing efficiency and patterns of insertions and deletions (indels), PCR products were generated using primers flanking the target sites, which were then subjected to next generation sequencing (NGS). Percent editing of corresponding sequences in unedited samples was typically less than 1% and never exceeded 3%.

Results:

Without being bound by theory, it is believed that targeted genetic disruption of the BCL11A erythroid enhancer region will relieve repression of γ-globin expression, allowing production of the red blood cells containing elevated HbF protein, (cells expressing fetal hemoglobin, e.g., expressing elevated levels of fetal hemoglobin, are sometimes referred to herein as “F-cells.” In embodiments, a cell is considered an F-cell if it produces as least 6 picograms fetal hemoglobin per cell). The elevated HbF prevents sickling of the red blood cells under deoxygenated conditions and will be therapeutic/curative for the patients of both β-thalassemia and SCD. Autologous hematopoietic stem cell transplantation (HSCT) with ex vivo genome edited HSC from SCD patients was also combined with stem cell expansion enhancing technology, e.g., an aryl hydrocarbon receptor (AHR) inhibitor, e.g., as described in WO2010/059401 (the contents of which are incorporated by reference in their entirety), e.g., Compound 4, to improve ex vivo expansion and increase the dose of gene modified HSC delivered.

For efficient genome editing via programmable nuclease, Cas9, the successful delivery of guide RNA (gRNA) and Cas9 protein into target cells and tissues is essential. Recent reports demonstrated that Cas9 ribonucleoprotein (RNP) complexes when delivered into target cells by electroporation can accomplish efficient and specific genome editing in several different cell types. Cas9-RNP complexes cleave chromosomal DNA almost immediately after delivery and are degraded rapidly in cells, reducing off-target effects. In contrast, use of plasmid and viral vector systems used to deliver Cas9 results in prolonged expression of the enzyme aggravating off-target effects associated with the system. Additionally, delivery of RNPs into the target cells requires no additional tools which would greatly facilitate translation of genome editing for therapeutic purposes in the clinic. Purified recombinant Cas9 protein and gRNA complexes (RNPs) were delivered into cultured HSPC and an overview experiments used are shown in FIG. 17.

Recombinant Cas9 protein was purified from Escherichia coli and complexed with synthetic dual gRNAs (dgRNA) that consist of crRNA and tracr to generate ribonucleoprotein (RNP) complexes. The list and of gRNAs used in the study are shown in Table 17 (e.g., gRNAs comprising the targeting domain of the indicated CRxxxxxx identifier). The RNP complexes were electroporated into CD34+ HSPC via electroporation as described under materials and methods. The cells were expanded prior to the delivery of RNP complexes. Actively dividing cells may facilitate uptake of RNP complexes delivered by electroporation.

TABLE 17 List of gRNAs targeting the BCL11A erythroid specific enhancer region used in the current study. All gRNA molecules were tested in duplicate in the dgRNA format as described in the materials and methods. % HbF+ (F % HbF+ (F Guide RNA cells), cells), % edited, % edited, targeting domain average of standard average of standard ID replicates deviation replicates deviation CR000308 27.7 0.5 52.8 0.7 CR000309 43.1 1.4 74.8 7.5 CR000310 28.6 0.1 65.1 3.6 CR000311 27.2 0.7 50.5 1.9 CR000312 47.9 1.0 87.8 0.9 CR000313 36.8 1.2 66.6 2.7 CR000314 32.7 0.1 39.8 0.5 CR000316_EH11 34.4 0.8 52.9 1.3 CR000317_EH4 50.7 0.4 82.7 2.5 CR001124 28.6 0.1 2.5 0.1 CR001125_EH12 42.3 0.4 94.0 0.9 CR001126_EH13 44.6 1.7 76.7 6.1 CR001127_EH14 33.3 0.1 26.1 3.3 CR001128_EH15 46.4 1.2 84.6 5.6 CR001129 25.3 0.8 3.6 0.4 CR001130 27.1 0.8 11.8 1.7 CR001131 28.6 0.0 35.6 8.5 None/control 22.4 0.6 n/a n/a g8 66.3 0.7 94.2 1.1

The genome edited and unedited HSPC were analyzed by flow cytometry for expression levels of fetal globin and two erythroid cell surface markers, transferrin receptor (CD71) and glycophorin A (CD235a) using antibodies conjugated to fluorescent dyes. The live cells were identified and gated by exclusion of Live Dead Violet. BCL11A erythroid specific enhancer region targeting resulted in increased percentage of erythroid cells containing HbF (up to 50.7%) compared to mock electroporated cells (22.4%) (Table 17). Induction of HbF positive cells by dgRNA including the targeting domain of g8 targeting exon 2 of BCL11A was also observed in parallel. Genomic PCR products of the BCL11A erythroid enhancer region were also subjected to next generation sequencing (NGS) to determine the percentage of edited alleles in the cell population. The dgRNA treatments that resulted in greater than 40% HbF+ cells had a range of 74.8% to 94.0% editing (Table 17). For the same targeting domain, the dgRNA in this Example differed in tracr and crRNA sequence from that in Example 3; however, the editing and HbF induction were similar across dgRNA formats for most targeting domains. Of note, CR000317_EH4 in the dgRNA format in the current study resulted in a high HbF induction to 50.7% HbF+ cells. An increase in HbF-containing erythrocytes derived from genome edited cells is likely to have positive therapeutic implications by reduced sickling.

Example 3.2. Optimization of gRNA Editing and Fetal Hemoglobin Upregulation Using gRNAs Targeting the +58 Region of the BCL11a Enhancer in HSPCs

Based on the % editing results from the comprehensive screen of gRNAs targeting the +58 region of the BCL11a Enhancer, 8 gRNA targeting domains were selected for further study and optimization. To test the effect of modifications to the gRNA molecules on % editing, erythroid differentiation, and fetal hemoglobin expression, different versions of the eight gRNA molecules targeting sites within the +58 region of the BCL11a enhancer region were designed. The following versions of of gRNAs comprising the targeting domain of CR00309, CR00311, CR00312, CR00316, CR01125, CR01126, CR01127, and CR01128 were made:

dgRNA (all Sequences Other than Those of the Targeting Domain as Described in Example 1):

-   -   1. Unmodified crRNA and unmodified tracr (“Unmodified” or         “Unmod”)     -   2. Unmodified crRNA and unmodified tracr, but with only the         5′-18nt of the indicated targeting domain (not the full 20 nt)         (“18nt”)     -   3. Three 3′ nt and three 5′ nt of crRNA modified with         phosphorothioate linkages, and unmodified tracr (“PS”)     -   4. Additional inverted abasic residue at both 5′- and 3′-end of         crRNA, and unmodified tracr (“Invd”)     -   5. Three 3′ nt and three 5′ nt of crRNA modified with         phosphorothioate linkages and with 2′-Omethyl groups, and         unmodified tracr (“OMePS”)     -   6. Three 3′ nt and three 5′ nt of crRNA modified with 2′-fluoro         group, and unmodified tmcr (“F”)     -   7. Three 3′ nt and three 5′ nt of crRNA modified with         phosphorothioate linkages and with 2′-fluoro group, and         unmodified tracr (“F—PS”)         sgRNA (all Sequences Other than Targeting Domain are as         Described in Example 1):     -   1. Unmodified sgRNA (“Unmodified” or “Unmod”)     -   2. Targeting domain consisting of only the 5′-18nt of the         indicated targeting domain (not the full 20 nt) (“18nt”)     -   3. Three 3′ nt and three 5′ nt of sgRNA modified with         phosphorothioate linkages (“PS”)     -   4. Additional inverted abasic residue at both 5′- and 3′-end of         sgRNA (“Invd”)     -   5. Three 3′ nt and three 5′ nt of sgRNA modified with         phosphorothioate linkages and with 2′-Omethyl groups (“OMePS”)     -   6. Three 3′ nt and three 5′ nt of sgRNA modified with 2′-fluoro         group (“F”)     -   7. Three 3′ nt and three 5′ nt of sgRNA modified with         phosphorothioate linkages and with 2′-fluoro group (“F—PS”)

All other reagents and methods were as described in Example 3. All results were run in duplicate, and the results are reported in FIGS. 28-32. FIG. 28A and FIG. 28B show the % editing, as measured by NGS, in CD34+ cells 2 days after electroporation of RNP comprising the indicated dual guide RNAs (dgRNAs). FIG. 29 shows the % editing, as measured by NGS, in CD34+ cells 2 days after electroporation of RNP comprising the indicated single guide RNAs (sgRNAs). FIG. 30 shows the % HbF positive cells as measured by flow cytometry at day 14 following transfer of edited CD34+ cells to erythroid differentiation medium, after electroporation of RNP comprising the indicated dual guide RNAs (dgRNAs). FIG. 31 shows the % HbF positive cells as measured by flow cytometry at day 14 following transfer of edited CD34+ cells to erythroid differentiation medium, after electroporation of RNP comprising the indicated single guide RNAs (sgRNAs). FIG. 32 shows the fold-expansion of edited cells after 14 days in the erythroid differentiation medium. These results indicate that many of the selected gRNA molecules, in both dgRNA and sgRNA formats, are capable of achieving genome editing at the target site with greater than 90% efficiency, and in some cases, with greater than 98% efficiency, when delivered to CD34+ cells as RNP via electroporation. As well, many of the selected gRNAs were able to achieve a greater than 20% increase in % F cells relative to unmodified cells (“mock”). Finally, although genome editing of BCL11A erythroid enhancer in HSPC lowered the expansion capabilities of erythroid cells, with the effect more pronounced with some gRNAs (e.g., CR00309) than other gRNAs (e.g., CR00312), most edited cell populations differentiated into erythrocytes were non-the-less capable of achieving between 500-1500 population doublings in 14 days in erythroid differentiation medium ex vivo, indicating that the edited cells may be therapeutically useful in treating hemoglobinopathies such as sickle cell disease or beta thalassemia in patients.

Example 4. HPFH Region Editing in Hematopoietic Stem and Progenitor Cells (HSPCs) Using CRISPR-Cas9 for Derepression of Fetal Globin Expression in Adult Erythroid Cells Methods:

Human CD34⁺ cell culture. Human CD34+ cells were isolated from G-CSF mobilized peripheral blood from adult donors (AllCells) using immunoselection (Miltenyi) according to the manufacturer's instructions and expanded for 4 to 6 days using StemSpan SFEM (StemCell Technologies; Cat no. 09650) supplemented with 50 ng/mL each of thrombopoietin (Tpo), Flt3 ligand (Flt-3L, Life Technologies, Cat. #PHC9413), human stem cell factor (SCF, Life Technologies, Cat. #PHC2113) and human interleukin-6 (IL-6, Life Technologies, Cat. #PHC0063), as well as 1× antibiotic/antimycotic (Gibco, Cat. #10378-016) and 500 nM compound 4. Throughout this example (including its subexamples), where the protocol indicates that cells were “expanded,” this medium was used. This medium is also referred to as “stem cell expansion medium,” or “expansion medium” throughout this example (including its subexamples).

Assembly of Cas9 and guide RNA ribonucleoprotein (RNP) complexes, preparation of HSPC, and electroporation of RNP into HSPC. Cas9-guide RNA ribonucleoprotein complexes (RNPs) were prepared immediately prior to electroporation. For formation of RNP using dual guide RNAs (dgRNAs), 3 μg of each of crRNA (in 2.24 μL) and tracr (in 1.25 μL) are first denatured at 95° C. for 2 min in separate tubes and then cooled to room temperature. For preparation of Cas9 protein, 6 μg of CAS9 protein (in 0.8 to 1 μL) was mixed with 0.5 μL of 5×CCE buffer (20 mM HEPES, 100 mM KCL, 5 mM MgCL2, 5% Glycerol and freshly added 1 mM DTT). Tracr was first mixed with the Cas9 preparation and incubated at 37° C. for 5 min. The crRNA was then added to Tracr/CAS9 complexes and incubated for 5 min at 37° C. For the None/control condition, vehicle rather than crRNA was added to the Tracr/CAS9 complexes. The HSPC were collected by centrifugation and resuspended in T buffer that comes with Neon electroporation kit (Invitrogen; Cat#: MPK1096) at a cell density of 5×10⁶/mL. The RNP was mixed with 20 μL of cells by pipetting up and down and incubated at RT for 2 min. The RNP/cell mixture (10 μL) was transferred into Neon electroporation probe. The electroporation was performed with Neon transfection system (Invitrogen; MPK5000S) using 1700 volts/20 milliseconds and 1 pulse. Duplicate 10 μL electroporations were performed.

In vitro erythropoiesis and FACS analysis for HbF containing erythroid cells. After electroporation, the cells were immediately transferred into 250 μL pre-warmed erythroid differentiation medium (EDM) consisting of IMDM (Hyclone, Cat. #SH30228.01), 330 μg/mL human holo-transferrin (Invitria Cat#777TRF029), 10 μg/mL recombinant human insulin (Gibco Cat#A1138211), 2 IU/mL heparin (Sigma, part #H3393), 5% human AB serum (Sigma, Cat# H4522), 125 ng/mL human erythropoietin (Peprotech #10779-058), and 1× antibiotic/antimycotic (Gibco, Cat. #10378-016). EDM was further supplemented with 1 μM hydrocortisone (Sigma H8672), 100 ng/mL human SCF (Life Technologies, Cat. #PHC2113), and 5 ng/mL human IL-3 (Peprotech #10779-598). After 2 days, the cell culture was diluted in fresh medium. Cultures were maintained for a total of 7 days, at which time the cells were analyzed by intracellular staining for HbF expression. Briefly, the cells were washed once with PBS, resuspended in LIVE/DEAD® Fixable Violet Dead Cell Stain (ThermoFisher L34963; 1:1000 in PBS) and incubated for 30 min. Cell were then washed and stained with anti-CD71-BV711 (Fisher Scientific Company Llc. BDB563767) and anti-CD235a-APC (BD 551336) antibodies for 30 min. The cells were then washed, followed by fixation with fixation buffer (Biolegend, Cat#420801) and permeabilized with 1× intracellular staining permeabilization wash buffer (Biolegend, Cat#421002) according to the manufacturers instructions. The cells were then incubated with 0.5 μL of anti-HbF-PE antibody (Life Technologies, part #MHFH04) in 50 μL of 1× intracellular staining perm wash buffer for 20 min at room temperature. The cells were washed twice with 2 mL of 1× intracellular staining Perm wash buffer and resuspend in staining buffer and analyzed on an LSRFortessa flow cytometer (BD Biosciences) for HbF expression. The results were analyzed using Flowjo and data were presented as % of HbF positive cells (F-cells) in the viable CD71 positive erythroid cell population.

Gene expression analysis. After 7 days of in vitro erythropoiesis as described, approximately 1×10⁵ cells were used to purify RNA using the Zymo Research ZR-96 quick RNA Kit (Zymo Cat# R1053). Up to 1 μg RNA was used for 1st strand synthesis using Quantiscript Reverse Transcription Kit (Qiagen, Cat#205313). Taq-man quantitative real-time PCR was performed using the 2× Taq-Man Fast Advance PR Mix (Life technologies, Cat#4444963) and Taq-Man Gene Expression Assays for GAPDH (Life technologies, ID# Hs02758991_g1, VIC), HBB (Life technologies, ID# Hs00747223_g1, VIC) and HBG2/HBG1 (Life technologies, ID# Hs00361131_g1, FAM), according to the suppliers protocol. The relative expression of each gene was normalized to GAPDH expression and reported as fold of None/control RNP-delivered samples by the ΔΔCt method. Alternatively, after conversion to a GAPDH normalized relative quantity of transcript (2̂-ΔCt), the HBG2/HBG1 expression level was calculated as a percentage of the sum of HBB and HBG2/HBG1 expression.

Genomic DNA preparation and next generation sequencing (NGS). Genomic DNA was prepared from edited and unedited HSPC at 48 hours post-electroporation using Quick Extract DNA Extraction Solution (Epicentre Cat # QE09050). To determine editing efficiency and patterns of insertions and deletions (indels), PCR products were generated using primers flanking the target sites, which were then subjected to next generation sequencing (NGS) as described in the literature. Percent editing of corresponding sequences in unedited samples (electroporated with RNPs consisting of Cas9 and Tracr only) was typically less than 1% and never exceeded 3%.

Results:

Without being bound by theory, it is believed that targeted genetic disruption of the HPFH region will relieve repression of γ-globin expression, allowing production of the red blood cells containing elevated HbF protein, (cells expressing fetal hemoglobin are sometimes referred to herein as “F-cells”). The elevated HbF prevents sickling of the red blood cells under deoxygenated conditions and will be therapeutic/curative for the patients of both β-thalassemia and SCD. Autologous hematopoietic stem cell transplantation (HSCT) with ex vivo genome edited HSC from SCD patients was also combined with stem cell expansion enhancing technology, e.g., an aryl hydrocarbon receptor (AHR) inhibitor, e.g., as described in WO2010/059401 (the contents of which are incorporated by reference in their entirety), e.g., Compound 4 to improve ex vivo expansion and increase the dose of gene modified HSC delivered.

For efficient genome editing via programmable nuclease, Cas9, the successful delivery of guide RNA (gRNA) and Cas9 protein into target cells and tissues is essential. Recent reports demonstrated that Cas9 ribonucleoprotein (RNP) complexes when delivered into target cells by electroporation can accomplish efficient and specific genome editing in several different cell types. Cas9-RNP complexes cleave chromosomal DNA almost immediately after delivery and are degraded rapidly in cells, reducing off-target effects. In contrast, use of plasmid and viral vector systems used to deliver Cas9 results in prolonged expression of the enzyme aggravating off-target effects associated with the system. Additionally, delivery of RNPs into the target cells requires no additional tools which would greatly facilitate translation of genome editing for therapeutic purposes in the clinic. Purified recombinant Cas9 protein and gRNA complexes (RNPs) were delivered into cultured HSPC and an overview experiments used are shown in FIG. 17.

Recombinant Cas9 protein was purified from Escherichia coli and complexed with synthetic dual gRNAs (dgRNA) that consist of crRNA and tracr to generate ribonucleoprotein (RNP) complexes. The list and sequences of gRNAs used in the study are shown in Table 16. The RNP complexes were electroporated into CD34+ HSPC via electroporation as described under materials and methods. The cells were expanded prior to the delivery of RNP complexes. Actively dividing cells may facilitate uptake of RNP complexes delivered by electroporation.

TABLE 16 List of gRNAs targeting the HPFH region used in the current study. All gRNA molecules were tested in duplicate in the dgRNA format described above, except for g8 (crRNA consisting of mN*mN*mN*rNrNrNrNrNrNrNrNrNrNr- NrNrNrNrNrNrNrGrUrUrUrUrArGrArGrCrUrArU*mG*m C*mU, where N's are the residues of the targeting domain, and modifications are indicated as follows: 2′O-Methyl (m) and Phosphorothioate Bond (*); with the tracr sequence SEQ ID NO: 7808) and None/control. The g8 and None/ control were tested in 16 replicates each. % HbF+ (F % HbF+ (F Guide RNA cells), cells), % CD71+, % CD71+, % edited, % edited, targeting average of standard average of standard average of standard domain ID replicates deviation replicates deviation replicates deviation CR001030 51.4 5.2 84.4 0.6 84.5 1.6 CR001095 49.3 1.8 82.7 2.5 66.1 1.4 CR001043 44.8 2.0 84.1 0.8 80.0 0.7 CR001029 43.7 1.3 82.2 0.7 86.6 2.7 CR001142 43.4 0.6 83.9 0.1 76.9 0.4 CR001028 42.9 1.3 84.8 0.5 91.7 0.5 CR001212 42.6 5.8 83.1 0.9 81.6 1.5 CR001036 42.4 1.3 82.6 0.6 91.5 5.0 CR001135 42.4 0.7 83.7 0.1 84.4 13.3 CR001221 41.8 1.7 80.8 0.4 83.9 1.4 CR001158 41.7 1.3 81.7 0.2 72.4 2.7 CR001090 41.3 0.1 85.5 0.8 87.2 1.2 CR001169 41.3 1.5 82.4 2.6 80.2 2.5 CR001089 40.9 0.6 82.8 6.6 81.7 0.3 CR001031 40.8 0.1 81.5 1.8 90.7 1.8 CR001092 40.8 2.2 84.1 0.1 43.0 1.1 CR001034 40.7 1.0 84.5 0.0 72.7 3.8 CR001068 40.7 2.3 85.7 0.4 90.5 0.9 CR001168 40.2 3.4 82.6 0.1 74.2 7.1 CR001171 40.1 1.6 83.4 0.4 63.8 1.6 CR001217 40.1 0.8 81.9 0.1 80.9 0.8 CR001023 39.6 3.2 82.2 0.8 90.2 0.7 CR001093 39.3 0.3 86 1.1 38.3 14.5 CR001080 39.2 3.4 87.1 1.1 32.4 1.1 CR001164 38.6 2.0 84.4 0.4 92.0 0.7 CR001178 38.6 1.2 82.6 2.4 61.1 0.6 CR001032 38.4 9.2 82.4 0.6 57.6 32.9 CR001100 38.4 1.8 81.7 0.2 29.6 2.4 CR001156 38.4 1.2 81.6 0.3 91.2 3.6 CR001159 38.4 1.8 81.8 0.2 65.5 0.7 CR001042 38.2 0.4 83.1 1.0 90.8 0.3 CR001065 38.2 0.0 85.2 2.0 86.5 0.2 CR001133 38.1 0.0 83.6 0.5 92.1 0.8 CR001173 38 1.5 81.7 1.1 72.5 5.0 CR001161 37.7 4.6 82.3 1.7 54.8 10.7 CR001138 37.6 7.6 83.7 0.7 69.4 28.9 CR001037 37.4 1.3 81.2 0.8 90.5 1.5 CR001098 37.4 1.2 85.6 1.5 95.0 0.2 CR001150 37.3 2.0 84.8 0.4 52.8 7.5 CR001160 37.3 0.5 81.4 1.5 65.9 1.6 CR001197 37.3 1.1 83.3 1.6 83.8 2.8 CR001170 37.2 1.3 83.7 1.2 47.3 0.3 CR001226 37 1.0 82.5 1.3 65.3 2.0 CR001018 36.9 0.8 80.9 0.8 97.2 0.0 CR001109 36.8 0.3 84.7 1.4 91.0 2.4 CR001219 36.8 0.6 82.5 0.1 75.9 0.2 CR001047 36.7 0.6 83.2 0.3 70.8 1.5 CR001101 36.6 3.3 81.7 0.1 50.6 3.8 CR001046 36.5 1.0 84 0.3 76.9 4.2 CR001021 36.4 0.3 82.2 0.4 79.5 2.9 CR001060 36.3 3.2 84.1 1.1 50.0 0.4 CR001074 36.3 1.6 87.3 1.8 56.5 4.9 CR001097 36.3 0.2 87.1 1.3 58.5 2.1 CR001099 36.1 4.0 85.8 1.8 89.8 0.3 CR001172 36.1 1.7 82.2 0.7 71.1 3.7 CR001195 36.1 0.8 83.4 0.2 67.2 2.7 CR001075 36 1.9 87.2 0.1 56.8 2.6 CR001143 35.9 3.7 83.5 0.4 56.7 9.2 CR001063 35.8 1.3 84.3 0.4 71.7 1.9 CR001225 35.5 0.4 83.1 0.5 81.1 4.2 CR001027 35.4 0.9 81.9 0.8 71.1 0.5 CR001073 35.4 1.6 86.5 1.6 56.3 5.9 CR001180 35.3 1.1 79.6 1.4 86.2 4.0 CR001182 35.3 0.8 81.8 0.2 72.5 3.9 CR001162 35.2 9.1 85 0.0 62.6 35.7 CR001026 35.1 1.0 82.4 0.2 97.0 0.3 CR001078 35 1.1 85 1.7 12.7 1.8 CR001025 34.9 0.3 81.9 1.5 55.5 3.8 CR001187 34.9 2.5 79.4 2.3 70.1 3.7 CR001081 34.8 1.4 87.5 4.0 27.0 0.7 CR001137 34.8 13.6 83.8 1.6 41.5 39.8 CR001174 34.8 0.5 81.8 0.6 34.1 3.2 CR001058 34.6 1.0 83.3 1.5 71.4 6.2 CR001188 34.6 1.3 82.6 1.2 64.0 2.2 CR001079 34.4 2.5 89.2 0.2 12.8 2.0 CR001179 34.4 3.2 82 0.4 81.4 4.3 CR001214 34 2.2 82.1 1.5 58.1 1.0 CR001139 33.9 1.9 83 2.5 70.3 0.4 CR001222 33.9 1.6 80.6 0.8 35.5 1.4 CR001096 33.8 0.1 85.6 2.2 77.5 1.0 CR001148 33.6 2.1 84.5 0.4 50.9 4.0 CR001140 33.5 0.4 84 1.4 66.3 1.5 CR001191 33.5 2.5 83.2 0.3 83.4 5.1 CR001227 33.5 2.3 79 0.2 56.3 0.1 CR001110 33.4 0.4 85.2 0.1 70.3 0.1 CR001220 33.4 1.7 81.4 0.4 72.4 3.3 CR001224 33.4 3.1 82.2 1.3 71.3 2.3 CR001033 33.2 0.3 81.9 0.6 63.6 8.1 CR001051 33.2 0.6 82.2 0.6 42.2 0.5 CR001106 33.2 0.2 82.6 3.0 46.9 2.0 CR001020 32.9 8.9 81.9 1.3 67.7 29.4 CR001022 32.9 0.8 82.4 1.6 91.5 0.3 CR001045 32.9 0.4 80.5 0.0 88.5 0.4 CR001198 32.9 0.5 81.3 1.8 96.8 0.5 CR001084 32.8 1.7 87.5 0.1 55.1 5.4 CR001111 32.6 1.0 84.2 2.5 78.1 1.4 CR001087 32.5 0.1 87.6 0.7 89.6 2.6 CR001107 32.5 0.4 83.3 1.8 46.5 2.2 CR001108 31.8 1.8 84.7 0.6 75.2 3.3 CR001205 31.7 2.3 81.3 6.2 2.7 1.7 CR001085 31.6 2.1 86 0.3 31.2 1.2 CR001166 31.5 0.5 83.6 0.8 86.9 0.3 CR001019 31.3 2.3 80.6 0.9 35.1 4.0 CR001076 31.3 0.5 86.6 0.2 96.3 0.3 CR001016 31.2 1.2 80.2 0.7 95.0 1.9 CR001035 31.1 1.8 83.5 1.3 80.0 0.9 CR001192 31 2.5 79.9 0.7 60.4 5.1 CR001091 30.7 2.8 85.3 0.6 72.4 7.6 CR001105 30.7 0.1 84.8 0.1 12.1 1.1 CR001185 30.7 0.7 82.7 0.4 36.7 0.2 CR001190 30.7 0.1 82.4 0.7 53.2 0.8 CR001024 30.6 0.4 81.8 0.7 97.0 0.6 CR001132 30.5 2.3 84.6 0.1 26.4 2.2 CR001189 30.4 1.9 83.1 0.3 42.0 0.6 CR001040 30.1 8.3 77.5 2.2 73.6 33.6 CR001146 30.1 1.5 83.8 0.1 88.1 2.1 CR001070 29.8 0.9 82.7 0.4 44.9 0.8 CR001213 29.8 1.8 81.9 0.2 48.4 4.4 CR001017 29.6 11.8 81.3 1.5 44.3 36.8 CR001077 29.5 0.9 87.2 2.5 14.3 0.5 CR001083 29.4 1.1 84.3 9.1 26.6 10.6 CR001082 29 0.7 87.6 1.5 17.7 0.0 CR001175 29 1.1 81.7 0.1 6.3 0.7 CR001144 28.9 0.4 82.6 0.9 38.8 1.1 CR001194 28.8 4.3 81.8 0.6 70.2 1.9 CR001157 28.5 1.1 81 1.3 29.2 4.2 CR001163 28.4 0.6 83.5 0.7 13.4 3.0 CR001151 28.2 0.6 84.6 1.6 51.8 2.3 CR001181 28.2 0.2 80.3 0.8 46.0 0.5 CR001061 28 2.9 82.6 0.4 53.6 5.8 CR001152 27.8 0.8 84.9 0.2 37.0 1.9 CR001094 27.7 9.2 74.6 12.7 85.2 2.1 CR001202 27.7 6.3 84 2.3 61.7 8.4 CR001149 27.6 1.7 84.1 0.6 10.8 1.3 CR001207 27.6 5.7 83.3 0.1 31.5 17.5 CR001134 27.2 1.6 83.2 1.3 2.3 0.2 CR001206 27.2 1.8 84.4 0.2 11.1 0.4 CR001067 27 18.4 84.2 2.6 6.0 0.8 CR001167 27 0.5 81.7 0.2 32.3 0.1 CR001209 27 0.8 81.5 2.5 14.8 0.2 CR001165 26.9 0.5 81.6 1.3 12.9 2.1 CR001044 26.8 7.2 78.2 4.3 28.5 20.7 CR001052 26.6 0.3 82.5 1.5 26.5 0.9 CR001062 26.6 0.7 78.7 2.8 39.1 5.3 CR001071 26.6 1.0 84.2 0.4 15.1 1.1 CR001210 26.6 2.1 80.1 3.3 58.6 2.2 CR001223 26.6 0.9 80.2 0.8 40.3 1.9 CR001057 26.5 6.5 82.4 0.1 25.0 18.9 CR001147 26.5 1.3 83.5 0.4 33.1 2.7 CR001186 26.4 2.1 79.6 3.8 40.5 2.1 CR001103 26.1 0.2 84.3 0.0 51.2 3.6 CR001199 25.9 0.8 80.9 1.5 89.3 1.4 CR001216 25.7 1.0 77.7 0.0 43.2 2.7 CR001041 25.6 1.8 78.9 4.8 22.4 2.1 CR001053 25.5 1.4 82.4 1.9 38.4 0.3 CR001086 25.4 0.6 84.4 0.9 30.4 0.6 CR001050 25.1 0.4 80.6 1.1 4.9 0.2 CR001136 25.1 0.7 82.3 1.0 9.1 1.1 CR001203 25.1 4.0 83.4 1.8 22.0 13.1 CR001211 24.8 1.1 83.3 0.4 5.0 1.0 CR001066 24.4 0.4 86.1 0.1 15.2 1.8 CR001145 24.4 1.0 83.5 0.9 16.4 8.9 CR001049 24.3 0.3 83.9 1.9 3.7 0.0 CR001176 24.3 0.6 81.9 0.6 29.0 1.4 CR001218 24.1 0.2 81.9 0.1 21.6 2.4 CR001141 23.8 0.5 82.8 0.4 4.1 0.8 CR001196 23.6 0.8 82.5 0.6 18.2 2.9 CR001184 23.5 0.4 81.1 0.4 43.5 1.6 CR001204 23.3 1.1 81.5 0.7 0.5 0.2 CR001069 23.1 1.1 85 0.0 16.2 0.3 CR001072 23 0.3 84.2 0.7 15.6 0.3 CR001102 22.8 1.7 84.7 1.6 58.1 4.8 CR001153 22.8 1.3 82.8 0.1 17.2 2.6 CR001177 22.8 0.5 82.2 0.9 2.0 0.2 CR001104 22.7 1.7 84.8 1.1 29.4 5.0 CR001064 22.6 1.1 82.1 1.0 35.8 5.2 CR001200 22.6 0.1 82 0.0 9.8 0.7 CR001154 22.4 0.0 82.2 1.3 8.0 1.1 CR001055 22.3 1.0 83.4 1.1 19.0 0.8 CR001054 22 1.1 83.5 1.0 11.3 1.4 CR001039 21.9 0.2 80.8 0.2 16.6 1.5 CR001183 21.6 0.7 81.4 0.8 13.3 0.1 CR001155 21.4 0.0 81.6 0.8 5.0 1.0 CR001059 21.1 0.6 82.5 1.2 4.6 0.3 CR001056 20.8 0.9 83.2 0.2 3.7 0.9 CR001193 20.5 0.9 80.4 0.9 4.8 0.2 CR001208 20.5 0.1 81.1 0.9 12.6 3.0 CR001201 20.1 1.7 81.7 0.6 10.7 0.7 CR001048 19.3 3.0 82.3 1.1 0.4 0.3 CR001215 19.2 0.2 81.2 2.3 5.6 2.2 CR001038 19.1 0.1 80.8 1.3 6.5 1.1 CR001088 18.8 5.9 67.3 2.7 74.6 2.3 None/control 21.0 2.0 82.9 1.9 n/a n/a g8 59.2 3.0 74.3 4.4 95.1 1.8

The genome edited and unedited HSPC were analyzed by flow cytometry for expression levels of fetal globin and two erythroid cell surface markers, transferrin receptor (CD71) and glycophorin A (CD235a) using antibodies conjugated to fluorescent dyes. The live cells were identified and gated by exclusion of Live Dead Violet. Genome editing did not adversely affect erythroid differentiation as the cultured cells showed percentages of CD71+ cells consistent with erythroblasts similar to uneditied cells. HPFH region targeting resulted in increased percentage of erythroid cells containing HbF (up to 51.4%) compared to mock electroporated cells (21.0%) (Table 16). Induction of HbF positive cells by dgRNA including the targeting domain of g8 targeting exon 2 of BCL11A was also observed in parallel. Genomic PCR products of the HPFH region were also subjected to next generation sequencing (NGS) to determine the percentage of edited alleles in the cell population. High genome editing percentages at the HFPH locus was observed in many of the cell cultures electroporated with RNPs containing Cas9, crRNA of the given targeting domain and Tracr (Table 16), but not in control cells with no targeting domain delivered (RNPs containing only Cas9 and Tracr). In particular, the dgRNA treatments that resulted in greater than 40% HbF+ cells had a range of 43.0% to 91.7% edited alleles (Table 16).

TABLE 18 Gene expression analysis of select cultures edited with gRNAs targeting the HPFH region in the current study. All gRNA molecules were tested in duplicate in the dgRNA format. Fetal gamma-globin (γ-globin, HBG2/ HBG1 genes), adult beta-globin (β-globin, HBB gene) and Glyceraldehyde- 3-Phosphate Dehydrogenase (GAPDH gene) expression were determined and reported as described in Materials and Methods. γ-globin β-globin expression, expression, % globin fold over fold over expression, Guide RNA Number of control control γ/(γ + β) targeting electroporation (average of (average of (average of domain ID replicates replicates) replicates) replicates) CR001030 2 3.8 0.91 26.6 CR001142 2 1.6 0.76 20.0 CR001212 2 2.2 0.58 18.6 CR001036 2 2.6 0.91 19.7 CR001221 2 2.3 0.79 15.2 CR001217 2 1.9 0.72 13.8 None/control 5 1 1 7.7

Some cultures in this study were also analyzed for hemoglobin gene expression. Of these targeting domains, fetal gamma-globin gene expression was induced 1.6 to 3.8-fold over None/control, which was accompanied by a modest reduction in adult beta-globin expression (0.58 to 0.91-fold of None/control) (Table 18). These effects together resulted in gamma-globin expression levels ranging from 13.8% to 26.6% of the total beta-type globins (γ/[γ+β]) in the cell population (Table 17), with relative fetal globin induction across targeting domains similar to that observed for HbF protein induction (Table 16). Either an increase in HbF/gamma-globin or an increase in HbF/gamma-globin together with a decrease in beta-globin (sickled globin) levels in erythrocytes derived from genome edited cells is likely to have therapeutic implications by reduced sickling.

Example 4.2

Methods: Methods are as in Example 4, with the Following Exceptions.

Assembly of Cas9 and guide RNA ribonucleoprotein (RNP) complexes, preparation of HSPC, and electroporation of RNP into HSPC. The HSPC collected by centrifugation were resuspended in P3 Primary Cell Solution (Lonza cat. No. PBP3-00675) at a cell density of 2.5×10⁶/mL. The RNP was mixed with 20 μL of cells by pipetting up and down and incubated at RT for 2 min. The RNP/cell mixture (20 μL) was electroporated using code CM-137 on the 4D-Nucleofector (Lonza).

Results:

Without being bound by theory, it is believed that targeted genetic disruption of the HPFH region will relieve repression of γ-globin expression, allowing production of the red blood cells containing elevated HbF protein, (cells expressing fetal hemoglobin are sometimes referred to herein as “F-cells”). The elevated HbF prevents sickling of the red blood cells under deoxygenated conditions and will be therapeutic/curative for the patients of both β-thalassemia and SCD. Autologous hematopoietic stem cell transplantation (HSCT) with ex vivo genome edited HSC from SCD patients was also combined with stem cell expansion enhancing technology, e.g., an aryl hydrocarbon receptor (AHR) inhibitor, e.g., as described in WO2010/059401 (the contents of which are incorporated by reference in their entirety), e.g., Compound 4 to improve ex vivo expansion and increase the dose of gene modified HSC delivered.

For efficient genome editing via programmable nuclease, Cas9, the successful delivery of guide RNA (gRNA) and Cas9 protein into target cells and tissues is essential. Recent reports demonstrated that Cas9 ribonucleoprotein (RNP) complexes when delivered into target cells by electroporation can accomplish efficient and specific genome editing in several different cell types. Cas9-RNP complexes cleave chromosomal DNA almost immediately after delivery and are degraded rapidly in cells, reducing off-target effects. In contrast, use of plasmid and viral vector systems used to deliver Cas9 results in prolonged expression of the enzyme aggravating off-target effects associated with the system. Additionally, delivery of RNPs into the target cells requires no additional tools which would greatly facilitate translation of genome editing for therapeutic purposes in the clinic. Purified recombinant Cas9 protein and gRNA complexes (RNPs) were delivered into cultured HSPC and an overview experiments used are shown in FIG. 17.

Recombinant Cas9 protein was purified from Escherichia coli and complexed with synthetic dual gRNAs (dgRNA) that consist of crRNA and tracr to generate ribonucleoprotein (RNP) complexes. The list of gRNAs used in the study are shown in Table 19. The RNP complexes were electroporated into CD34+ HSPC via electroporation as described under materials and methods. The cells were expanded prior to the delivery of RNP complexes. Actively dividing cells may facilitate uptake of RNP complexes delivered by electroporation.

TABLE 19 List of gRNAs targeting the HPFH region used in the current study. All gRNA molecules were tested in the dgRNA format (except for g8 which was tested in the dgRNA format using: crRNA consisting of mN*mN*mN*rNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrGrUrUrUr UrArGrArGrCrUrArU*mG*mC*mU, where N's are the residues of the targeting domain, and modifications are indicated as follows: 2′O-Methyl (m) and Phosphorothioate Bond (*); with the tracr sequence SEQ ID NO: 7808). Guide RNA targeting % HbF+ (F domain ID cells) % CD71+ CR003037 46.6 80.3 CR003033 45.4 75.9 CR003038 42.9 77.6 CR003035 42.1 77.8 CR003087 42.1 76.7 CR003085 41.8 77.6 CR003052 39.9 80.5 CR003080 38.0 80.1 CR003081 35.3 80.6 CR003031 34.8 77.7 CR003056 34.3 78.3 CR003070 33.9 81.2 CR003089 33.8 77.8 CR003065 33.0 76.4 CR003075 33.0 75.2 CR003088 33.0 77.3 CR003041 32.1 76.2 CR003039 31.9 75.7 CR003044 30.6 77.7 CR003084 29.7 77.2 CR003073 29.5 76.9 CR003066 29.3 77.9 CR003082 29.3 78.6 CR003067 29.2 78.1 CR003074 29.1 77.5 CR003095 28.8 80.4 CR003083 28.3 76.6 CR003030 27.9 78.4 CR003069 27.7 78.9 CR003055 27.6 78.9 CR003058 27.6 78.8 CR003054 27.5 79.0 CR003029 27.1 78.4 CR003086 27.1 76.6 CR003063 27.0 76.0 CR003071 26.5 79.5 CR003079 26.5 78.0 CR003042 26.4 77.0 CR003045 26.3 78.0 CR003034 25.9 76.8 CR003027 25.7 79.2 CR003043 25.0 76.0 CR003032 24.9 77.9 CR003040 24.9 75.7 CR003028 24.8 78.6 CR003048 24.8 80.4 CR003057 24.7 79.0 CR003096 24.6 78.9 CR003077 24.4 77.7 CR003036 24.3 76.8 CR003049 24.3 78.4 CR003047 24.0 78.2 CR003059 23.9 80.2 CR003051 23.7 77.2 CR003053 23.7 76.9 CR003091 23.7 80.2 CR003093 23.7 79.2 CR003060 23.6 78.9 CR003072 23.6 77.7 CR003076 23.6 78.0 CR003078 23.6 78.0 CR003064 23.4 75.9 CR003046 23.3 80.5 CR003092 22.9 81.7 CR003090 22.7 79.7 CR003050 22.6 77.2 CR003062 22.1 76.5 CR003061 21.5 76.3 CR003068 21.5 78.8 CR003094 21.0 79.6 None/control 18.9 77.0 replicate 1 None/control 21.1 79.7 replicate 2 g8 replicate 1 56.8 65.4 g8 replicate 2 56.4 65.8

The genome edited and unedited HSPC were analyzed by flow cytometry for expression levels of fetal globin and two erythroid cell surface markers, transferrin receptor (CD71) and glycophorin A (CD235a) using antibodies conjugated to fluorescent dyes. The live cells were identified and gated by exclusion of Live Dead Violet. Genome editing did not adversely affect erythroid differentiation as the cultured cells showed percentages of CD71+ cells consistent with erythroblasts similar to uneditied cells. HPFH region targeting resulted in increased percentage of erythroid cells containing HbF (up to 46.6%) compared to mock electroporated cells (18.9 and 21.1%) (Table 19). Induction of HbF positive cells by dgRNA including the targeting domain of g8 targeting exon 2 of BCL11A was also observed in parallel.

Finally, the indel pattern created at or near the target site for dgRNAs comprising the targeting domains of CR003031, CR003033, CR003035, CR003037, CR003038, CR003052, CR003085 were assessed by NGS. The top 5 most frequent indels at each location are shown in Table 27.

TABLE 27 5 most frequent indels at each taget sequence after exposure to RNP comprising the indicated gRNA molecule. Each gRNA was tested in dgRNA. Capital letters are the naturally occurring nucleotides at and near the target sequence. Deletions relative to the unmodified target sequence are shown as “—”; insertions are shown as lowercase letters. dgRNA targeting % of all Indel domain Variant Read (Genomic Sequence) reads Length CR003031 ACTGTTGATTAGAGGTAGGGAAATGATTTTAATCTGTGACCTTGG------- 9.74% −7 GCAAGTAGCTATCTAATGACTAAAATGG CR003031 ACTGTTGATTAGAGGTAGGGAAATGATTTTAATCTGTGACCTTGGTtGAATGGGC 7.82% 1 AAGTAGCTATCTAATGACTAAAATGG CR003031 ACTGTTGATTAGAGGTAGGGAAATGATTTTAATCTGTGACCTTG--- 2.19% −3 AATGGGCAAGTAGCTATCTAATGACTAAAATGG CR003031 ACTGTTGATTAGAGGTAGGGAAATGATTTTAATCTGTGACCTTG- 1.37% −1 TGAATGGGCAAGTAGCTATCTAATGACTAAAATGG CR003031 ACTGTTGATTAGAGGTAGGGAAATGATTTTAATCTGTGA--------- 1.33% −9 ATGGGCAAGTAGCTATCTAATGACTAAAATGG CR003031 . . . . . . CR003033 ATGGGCAAGTAGCTATCTAATGACTAAAATGGAA---------- 25.21% −10 GAGAAACAGTTTTAGTATAACAAGTGAAATACCCAT CR003033 ATGGGCAAGTAGCTATCTAATGACTAAAATGGAAAAaCACTGGAAGAGAAACAGT 7.77% 1 TTTAGTATAACAAGTGAAATACCCAT CR003033 ATGGGCAAGTAGCTATCTAATGACTAAAATGGAA-- 5.72% −2 CACTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACCCAT CR003033 ATGGGCAAGTAGCTATCTAATGACTAAAATGGAAAAC-- 2.94% −2 TGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACCCAT CR003033 ATGGGCAAGTAGCTATCTAATGACTAAAATGGAAAACcACTGGAAGAGAAACAGT 1.68% 1 TTTAGTATAACAAGTGAAATACCCAT CR003033 . . . . . . CR003035 CACTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACCCATG--- 10.87% −3 AGTCTGAGGTGCCTATAGGACATCTATATAAA CR003035 CACTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACCCAT- 2.62% −1 CTGAGTCTGAGGTGCCTATAGGACATCTATATAAA CR003035 CACTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACCCA-- 2.04% −2 CTGAGTCTGAGGTGCCTATAGGACATCTATATAAA CR003035 CACTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACCCATG-- 1.79% −2 GAGTCTGAGGTGCCTATAGGACATCTATATAAA CR003035 CACTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACCC---- 1.77% −4 TGAGTCTGAGGTGCCTATAGGACATCTATATAAA CR003035 . . . . . . CR003037 TAACAAGTGAAATACCCATGCTGAGTCTGAGG---------- 7.19% −10 ACATCTATATAAATAAGCCCAGTACATTGTTTGATATA CR003037 TAACAAGTGAAATACCCATGCTGAGTCTGAGGTGCC- 6.13% −1 ATAGGACATCTATATAAATAAGCCCAGTACATTGTTTGATATA CR003037 TAACAAGTGAAATACCCATGCTGAGTCTGAGGTGCCcTATAGGACATCTATATAA 4.17% 1 ATAAGCCCAGTACATTGTTTGATATA CR003037 TAACAAGTGAAATACCCATGCTGAGTCTGAGGTGCCTtATAGGACATCTATATAA 3.89% 1 ATAAGCCCAGTACATTGTTTGATATA CR003037 TAACAAGTGAAATACCCATGCTGAGTCTGAGGTGC- 3.72% −1 TATAGGACATCTATATAAATAAGCCCAGTACATTGTTTGATATA CR003037 . . . . . . CR003038 TAGTATAACAAGTGAAATACCCATGCTGAGTCTGAGGTGCCTATA---------- 14.85% −11 -TAAATAAGCCCAGTACATTGTTTG CR003038 TAGTATAACAAGTGAAATACCCATGCTGAGTCTGAGGTGCCTATAG- 6.25% −1 ACATCTATATAAATAAGCCCAGTACATTGTTTG CR003038 TAGTATAACAAGTGAAATACCCATGCTGAGTCTGAGGTGCCTAT- 3.99% −1 GGACATCTATATAAATAAGCCCAGTACATTGTTTG CR003038 TAGTATAACAAGTGAAATACCCATGCTGAGTCTGAGGTGCCTATAGGgACATCTA 2.83% 1 TATAAATAAGCCCAGTACATTGTTTG CR003038 TAGTATAACAAGTGAAATACCCATGCTGAGTCTGAGGTGCCTATAaGGACATCTA 2.76% 1 TATAAATAAGCCCAGTACATTGTTTG CR003038 . . . . . . CR003052 TCAGAGGTTAGAAATCAGAGTTGGGAATTGGGATTA-- 14.04% −2 CAGGCTGTATTTAAGAGTTTAGATATAACTGTGAATCCAAGA CR003052 TCAGAGGTTAGAAATCAGAGTTGGGAATTGGGATTAaTACAGGCTGTATTTAAGA 2.94% 1 GTTTAGATATAACTGTGAATCCAAGA CR003052 TCAGAGGTTAGAAATCAGAGTTGGGAATTGGGATT- 2.41% −1 TACAGGCTGTATTTAAGAGTTTAGATATAACTGTGAATCCAAGA CR003052 TCAGAGGTTAGAAATCAGAGTTGGGAATTGGGATTATtACAGGCTGTATTTAAGA 2.37% 1 GTTTAGATATAACTGTGAATCCAAGA CR003052 TCAGAGGTTAGAAATCAGAGTTGGGAATTGGGATTAaaTACAGGCTGTATTTAAG 2.28% 2 AGTTTAGATATAACTGTGAATCCAAGA CR003052 . . . . . . CR003085 TGTAAGGAGGATGAGCCACATGGTATGGGAGGTAT- 12.03% −1 CTAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTAC CR003085 TGTAAGGAGGATGAGCCACATGGTATGGGAGG---------- 8.70% −10 ACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTAC CR003085 TGTAAGGAGGATGAGCCACATGGTATGGGA------------- 4.42% −13 CTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTAC CR003085 TGTAAGGAGGATGAGCCACATGGTATGGGAGGTATAaCTAAGGACTCTAGGGTCA 4.38% 1 GAGAAATATGGGTTATATCCTTCTAC CR003085 TGTAAGGAGGATGAGCCACATGGTATGGGAGGTA----- 3.41% −5 AGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTAC CR003085 . . . . . . CR003087 GATGAGCCACATGGTATGGGAGGTATACTAAGGACTtCTAGGGTCAGAGAAATAT 24.73% 1 GGGTTATATCCTTCTACAAAATTCAC CR003087 GATGAGCCACATGGTATGGGAGGTATACTA--------- 15.83% −9 GGGTCAGAGAAATATGGGTTATATCCTTCTACAAAATTCAC CR003087 GATGAGCCACATGGTATGGGAGGTATACTAAGG-------- 8.50% −8 GTCAGAGAAATATGGGTTATATCCTTCTACAAAATTCAC CR003087 GATGAGCCACATGGTATGGGAGGTATACTAAGGACT-- 7.07% −2 AGGGTCAGAGAAATATGGGTTATATCCTTCTACAAAATTCAC CR003087 GATGAGCCACATGGTATGGGAGGTATACTAAGG--------- 1.75% −9 TCAGAGAAATATGGGTTATATCCTTCTACAAAATTCAC CR003087 . . . . . .

These results support the conclusion from earlier experiments described herein that small indels (e.g., in this case, indels from 1-20 nucleotides) in the HPFH region targeted by the indicated gRNA molecule can have a significant impact on expression and production of HbF. An increase in HbF-containing erythrocytes derived from genome edited cells is likely to have therapeutic implications by reduced sickling.

Example 4.3

Methods: Methods are as in Example 4, with the Following Exceptions.

Human CD34⁺ cell culture. Human CD34+ cells were expanded for 3 days prior to RNP delivery in expansion medium.

Assembly of Cas9 and guide RNA ribonucleoprotein (RNP) complexes, preparation of HSPC, and electroporation of RNP into HSPC. The HSPC collected by centrifugation were resuspended in P3 Primary Cell Solution (Lonza cat. No. PBP3-00675) at a cell density of 6.4×10⁶/mL. The RNP was mixed with 20 μL of cells by pipetting up and down and incubated at RT for 2 min. The RNP/cell mixture (20 μL) was electroporated using code CM-137 on the 4D-Nucleofector (Lonza). Electroporations were performed in duplicate. The Tracr was SEQ ID NO: 7808 and the crRNA had the following format with 2′O-Methyl (m) and Phosphorothioate Bond (*) modifications indicated: mN*mN*mN*rNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrGrUrUrUrUrArGrArGrCrUrArU*mG*m C*mU, where N's are the nucleotides of the targeting domain.

In vitro erythropoiesis and FACS analysis for HbF containing erythroid cells. After electroporation, the cells were immediately transferred into pre-warmed medium consisting of EDM and supplements. During days 0-7 of culture, EDM was further supplemented with 1 μM hydrocortisone (Sigma. H8672), 100 ng/mL human SCF (Life Technologies, Cat. #PHC2113), and 5 ng/mL human IL-3 (Peprotech #10779-598). During days 7-11 of culture, EDM was supplemented with 100 ng/mL of human SCF only. During days 11-21 of culture, EDM had no additional supplements. Cell cultures were initiated at 2.6×10⁴ cells per ml on day 0, adjusted to 4.0×10⁴ cells per ml on day 7, and adjusted to 1.0×10⁶ cells per ml on day 11. On days 14 and 19, the media was replenished. Viable cells were counted at 1, 4, 7, 11, 14 and 21 days post-RNP delivery. All viable cell counts were determined by flow cytometry using AccuCheck Counting Beads (ThermoFisher cat. No. PCB100) with inviable cells discriminated by DAPI (4′,6-Diamidino-2-Phenylindole) staining. On days 7, 16 and 21 of the culture, the cells (1×10⁵) were analyzed by intracellular staining for HbF expression. On days 16 and 21 intracellular staining for HbF expression did not include anti-CD71 and anti-CD235a antibodies, and % of HbF positive cells (F-cells) in the entire viable cell population was reported. On day 21 LIVE/DEAD® Fixable Near-IR Dead Cell Stain (ThermoFisher L34975) was used as the viability dye.

Genomic DNA preparation and next generation sequencing (NGS). Genomic DNA was prepared from edited and unedited HSPC at 7 days post-electroporation using Quick Extract DNA Extraction Solution (Epicentre Cat # QE09050).

Results:

Without being bound by theory, it is believed that targeted genetic disruption of the HPFH region will relieve repression of γ-globin expression, allowing production of the red blood cells containing elevated HbF protein, (cells expressing fetal hemoglobin are sometimes referred to herein as “F-cells”). The elevated HbF prevents sickling of the red blood cells under deoxygenated conditions and will be therapeutic/curative for the patients of both β-thalassemia and SCD. Autologous hematopoietic stem cell transplantation (HSCT) with ex vivo genome edited HSC from SCD patients was also combined with stem cell expansion enhancing technology, e.g., an aryl hydrocarbon receptor (AHR) inhibitor, e.g., as described in WO2010/059401 (the contents of which are incorporated by reference in their entirety), e.g., Compound 4 to improve ex vivo expansion and increase the dose of gene modified HSC delivered.

For efficient genome editing via programmable nuclease, Cas9, the successful delivery of guide RNA (gRNA) and Cas9 protein into target cells and tissues is essential. Recent reports demonstrated that Cas9 ribonucleoprotein (RNP) complexes when delivered into target cells by electroporation can accomplish efficient and specific genome editing in several different cell types. Cas9-RNP complexes cleave chromosomal DNA almost immediately after delivery and are degraded rapidly in cells, reducing off-target effects. In contrast, use of plasmid and viral vector systems used to deliver Cas9 results in prolonged expression of the enzyme aggravating off-target effects associated with the system. Additionally, delivery of RNPs into the target cells requires no additional tools which would greatly facilitate translation of genome editing for therapeutic purposes in the clinic. Purified recombinant Cas9 protein and gRNA complexes (RNPs) were delivered into cultured HSPC and an overview experiments used are shown in FIG. 17.

Recombinant Cas9 protein was purified from Escherichia coli and complexed with synthetic dual gRNAs (dgRNA) that consist of crRNA and tracr to generate ribonucleoprotein (RNP) complexes. The list of gRNAs used in the study are shown in Table 20. The RNP complexes were electroporated into CD34+ HSPC via electroporation as described under materials and methods. The cells were expanded prior to the delivery of RNP complexes. Actively dividing cells may facilitate uptake of RNP complexes delivered by electroporation.

TABLE 20 Relative viable cell proliferation in the current study. Individual electroporation replicates are shown. All gRNA molecules were tested in the dgRNA format using the tracr SEQ ID NO: 7808, and the crRNA had the following format with 2′O-Methyl (m) and Phosphorothioate Bond (*) modifications indicated: mN*mN*mN*rNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrGrUrUr- UrUrArGrArGrCrUrArU*mG*m C*mU, where N's are the nucleotides of the targeting domain. (n.d. not determined) Guide RNA targeting domain ID and replicate Day 0 Day 1 Day 4 Day 7 Day 11 Day 14 Day 21 CR001030 replicate 1 1 0.66 4.3 43.1 627 680 772 CR001030 replicate 2 1 0.65 4.0 38.4 651 694 880 CR001028 replicate 1 1 0.61 4.0 33.2 588 509 742 CR001028 replicate 2 1 0.77 6.1 44.9 724 759 838 CR001095 replicate 1 1 0.66 4.0 40.7 665 503 835 CR001095 replicate 2 1 0.96 5.2 42.2 651 777 n.d. CR001212 replicate 1 1 0.58 3.4 33.6 465 414 495 CR001212 replicate 2 1 0.74 3.6 32.4 490 519 572 g8 replicate 1 1 0.61 4.4 31.8 221 341 91 g8 replicate 2 1 0.60 5.2 33.2 269 270 103 None/control replicate 1 1 0.79 7.6 58.5 741 862 707 None/control replicate 2 1 0.71 8.2 51.4 923 1204 1075

The genome edited and unedited HSPC were analyzed for proliferation in a three-stage erythroid differentiation cell culture protocol. Percent cell recovery at 1 day after electroporation ranged from 58% to 96% and was similar across conditions, including the unedited but electroporated control (Table 20). Proliferation was suppressed in the cells edited by dgRNA including the targeting domain of g8 targeting exon 2 of BCL11A (10-12% of unedited control at day 21, Table 20), but proliferation of cells edited with the included HPFH region targeting dgRNAs was similar to control (47-99% of unedited control at day 21, Table 20).

TABLE 21 HbF induction in the current study. Individual electroporation replicates are shown. All gRNA molecules were tested in the dgRNA format. All gRNA molecules were tested in the dgRNA format using the tracr SEQ ID NO: 7808, and the crRNA had the following format with 2′O- Methyl (m) and Phosphorothioate Bond (*) modifications indicated: mN*mN*mN*rNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrGrUrUrUr UrArGrArGrCrUrArU*mG*mC*mU, where N's are the nucleotides of the targeting domain. (n.d. not determined) Guide RNA targeting % % % HbF+ % HbF+ % HbF+ domain edited, CD71+, (F cells), (F cells), (F cells), ID and replicate Day 7 Day 7 Day 7 Day 16 Day 21 CR001030 90.7 91.2 61.0 45.4 53.7 replicate 1 CR001030 90.1 91.1 63.9 44.3 55.9 replicate 2 CR001028 91.9 90.0 61.6 40.9 52.0 replicate 1 CR001028 87.6 90.7 56.3 46.6 45.8 replicate 2 CR001095 25.7 91.4 51.3 36.8 43.7 replicate 1 CR001095 30.5 91.1 52.5 42.7 n.d. replicate 2 CR001212 86.2 90.8 57.5 38.7 45.2 replicate 1 CR001212 80.9 90.4 54.7 36.5 42.7 replicate 2 g8 replicate 1 95.3 84.6 70.7 71.9 63.4 g8 replicate 2 94.3 82.6 70.0 72.6 54.8 None/control n/a 94.0 27.1 24.4 22.8 replicate 1 None/control n/a 93.8 26.2 25.7 21.1 replicate 2

The genome edited and unedited HSPC were analyzed by flow cytometry for expression levels of fetal globin and two erythroid cell surface markers, transferrin receptor (CD71) and glycophorin A (CD235a) using antibodies conjugated to fluorescent dyes. The live cells were identified and gated by exclusion of Live/Dead Fixable Dead Cell Stain. Genome editing did not adversely affect erythroid differentiation as the cultured cells showed percentages of CD71+ cells consistent with erythroblasts similar to uneditied cells at day 7 of differentiation. Cultures treated with the included HPFH region targeting dgRNAs resulted in increased percentage of erythroid cells containing HbF compared to mock electroporated cells throughout the 21 day culture period (Table 21). Induction of HbF positive cells by dgRNA including the targeting domain of g8 targeting exon 2 of BCL11A was also observed in parallel. Genomic PCR products of the HPFH region were also subjected to next generation sequencing (NGS) to determine the percentage of edited alleles in the cell population. Genome editing at the HFPH locus was observed in cell cultures electroporated with RNPs containing Cas9, crRNA of the given targeting domain and Tracr (Table 21), but not in control cells with no targeting domain delivered (RNPs containing only Cas9 and Tmcr). An increase in HbF-containing erythrocytes derived from genome edited cells is likely to have therapeutic implications by reduced sickling.

Example 4.4

Methods: Methods are as in Example 4, with the Following Exceptions.

Human CD34⁺ cell culture Human CD34+ cells were expanded for 3 to 6 days prior to RNP delivery in expansion medium, depending on study.

Assembly of Cas9 and guide RNA ribonucleoprotein (RNP) complexes, preparation of HSPC, and electroporation of RNP into HSPC. For some studies, the RNP complexes were delivered using the 4D-Nucleofector (Lonza). In those studies, the HSPC collected by centrifugation were resuspended in P3 Primary Cell Solution (Lonza cat. No. PBP3-00675) at a cell density of 2.2×10⁶/mL to 6.4×10⁶/mL, depending on study. The RNP was mixed with 20 μL of cells by pipetting up and down and incubated at RT for 2 min. The RNP/cell mixture (20 μL) was electroporated using code CM-137 on the 4D-Nucleofector (Lonza). Electroporations were performed in duplicate. The dgRNA format varied between studies and is indicated in Table 22 by the following notation. Form A is the dgRNA format described above in Example 1, with the targeting domain sequence indicated. Form B is a dgRNA format using a crRNA of rNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrGrUrUrUrUrArGrArGrCrUrArUrGrCrU, where r indicates an RNA base and the N's correspond to the indicated targeting domain sequence, and a tracr consisting of SEQ ID NO: 7808. Form C is a dgRNA format using crRNA of the sequence mN*mN*mN*rNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrGrUrUrUrUrArGrArGrCrUrArU*mG*m C*mU, where r indicates an RNA base, N's corresponds to the indicated targeting domain sequence, m indicates a base with 20-Methyl modification, and * indicates a phosphorothioate bond, and the tracr consists of SEQ ID NO: 7808.

In vitro erythropoiesis and FACS analysis for HbF containing erythroid cells. In one study, cell cultures were initiated at 2.6×10⁴ cells per ml on day 0. For those initiated by seeding directly into 250 μl (as described in Example 4), the cell culture was diluted in fresh medium after 1 to 3 days, depending on the study.

Genomic DNA preparation and next generation sequencing (NGS). Genomic DNA was prepared from edited and unedited HSPC at 24 hours to 7 days post-electroporation, depending on the study, using Quick Extract DNA Extraction Solution (Epicentre Cat # QE09050).

Results:

Without being bound by theory, it is believed that targeted genetic disruption of the HPFH region will relieve repression of γ-globin expression, allowing production of the red blood cells containing elevated HbF protein, (cells expressing fetal hemoglobin are sometimes referred to herein as “F-cells”). The elevated HbF prevents sickling of the red blood cells under deoxygenated conditions and will be therapeutic/curative for the patients of both β-thalassemia and SCD. Autologous hematopoietic stem cell transplantation (HSCT) with ex vivo genome edited HSC from SCD patients was also combined with stem cell expansion enhancing technology, e.g., an aryl hydrocarbon receptor (AHR) inhibitor, e.g., as described in WO2010/059401 (the contents of which are incorporated by reference in their entirety), e.g., Compound 4 to improve ex vivo expansion and increase the dose of gene modified HSC delivered.

For efficient genome editing via programmable nuclease, Cas9, the successful delivery of guide RNA (gRNA) and Cas9 protein into target cells and tissues is essential. Recent reports demonstrated that Cas9 ribonucleoprotein (RNP) complexes when delivered into target cells by electroporation can accomplish efficient and specific genome editing in several different cell types. Cas9-RNP complexes cleave chromosomal DNA almost immediately after delivery and are degraded rapidly in cells, reducing off-target effects. In contrast, use of plasmid and viral vector systems used to deliver Cas9 results in prolonged expression of the enzyme aggravating off-target effects associated with the system. Additionally, delivery of RNPs into the target cells requires no additional tools which would greatly facilitate translation of genome editing for therapeutic purposes in the clinic. Purified recombinant Cas9 protein and gRNA complexes (RNPs) were delivered into cultured HSPC and an overview experiments used are shown in FIG. 17.

Recombinant Cas9 protein was purified from Escherichia coli and complexed with synthetic dual gRNAs (dgRNA) that consist of crRNA and tracr to generate ribonucleoprotein (RNP) complexes. The list of gRNAs used in the studies are shown in Table 22. The RNP complexes were electroporated into CD34+ HSPC via electroporation as described under materials and methods. The cells were expanded prior to the delivery of RNP complexes. Actively dividing cells may facilitate uptake of RNP complexes delivered by electroporation.

TABLE 22 Summary data for multiple studies evaluating indicated gRNAs targeting the HPFH region and controls. All gRNA molecules were tested in dgRNA formats. Details of the dgRNA formats in the indicated studies are specified as described above. Note that evaluations 4 and 5 were performed in parallel and thus share control conditions. Guide RNA targeting Evaluation number domain ID 1 2 3 4 5 6 7 8 CR001028 Format A A B B C C Replicates 2 2 2 2 2 2 % HbF+ (F cells), 42.9 39.7 47.4 51.1 55.3 59.0 average of replicates % edited, average of 91.7 78.0 87.5 90.9 84.6 89.8 replicates CR001030 Format A A B B C C C C Replicates 2 2 2 2 2 2 2 2 % HbF+ (F cells), 51.4 48.7 50.9 51.8 58.0 39.7 50.6 62.5 average of replicates % edited, average of 84.5 61.8 74.3 75.0 85.6 94.1 85.4 90.4 replicates CR001036 Format A A B Replicates 2 2 2 % HbF+ (F cells), 42.4 40.8 43.3 average of replicates % edited, average of 84.4 78.3 92.6 replicates CR001043 Format A A B Replicates 2 2 2 % HbF+ (F cells), 44.8 33.0 42.9 average of replicates % edited, average of 80.0 42.7 87.7 replicates CR001080 Format A A C Replicates 2 2 2 % HbF+ (F cells), 39.2 34.9 49.3 average of replicates % edited, average of 32.4 24.0 41.6 replicates CR001095 Format A A B B C C C C Replicates 2 2 1 2 2 2 2 2 % HbF+ (F cells), 49.3 41.5 47 51.8 51.8 32.9 46.8 51.9 average of replicates % edited, average of 66.1 49.8 65.1 64.6 64.2 66.8 56.1 28.1 replicates CR001137 Format A A C C Replicates 2 2 2 2 % HbF+ (F cells), 34.8 45.6 31.0 40.8 average of replicates % edited, average of 41.5 46.9 69.0 57.9 replicates CR001142 Format A A C Replicates 2 2 2 % HbF+ (F cells), 43.4 45.5 48.1 average of replicates % edited, average of 76.9 63.7 89.2 replicates CR001158 Format A A C Replicates 2 2 2 % HbF+ (F cells), 41.7 36.9 44.6 average of replicates % edited, average of 72.4 43.9 78.4 replicates CR001212 Format A A B B C C C C Replicates 2 2 2 2 2 2 2 2 % HbF+ (F cells), 42.6 46.9 43.8 44.5 53.5 39.4 47.1 56.1 average of replicates % edited, average of 81.6 58.1 48.6 47.5 69.2 82.0 67.0 83.6 replicates CR001217 Format A A C C Replicates 2 2 2 2 % HbF+ (F cells), 40.1 41.5 29.9 45.9 average of replicates % edited, average of 80.9 50.3 89.0 82.1 replicates CR001221 Format A A B B C Replicates 2 2 1 2 2 % HbF+ (F cells), 41.8 45.2 44.6 46.2 48.6 average of replicates % edited, average of 83.9 71.1 73.6 70.7 92.1 replicates g8 Format C C C C C C C Replicates 16 2 2 2 2 2 2 % HbF+ (F cells), 59.2 60.0 66.3 64.7 64.7 55.8 70.4 average of replicates % edited, average of 95.1 85.4 94.2 94.6 94.6 91.7 94.8 replicates None/control Format n/a n/a n/a n/a n/a n/a n/a n/a Replicates 16 2 2 2 2 2 2 2 % HbF+ (F cells), 21.0 20.3 22.4 22.4 22.4 13.9 24.0 26.7 average of replicates % edited, average of n/a n/a n/a n/a n/a n/a n/a n/a replicates

The genome edited and unedited HSPC were analyzed by flow cytometry for expression levels of fetal globin and two erythroid cell surface markers, transferrin receptor (CD71) and glycophorin A (CD235a) using antibodies conjugated to fluorescent dyes. The live cells were identified and gated by exclusion of Live Dead Violet. HPFH region targeting resulted in increased percentage of erythroid cells containing HbF compared to mock electroporated cells, a consistent result across multiple evaluations and dgRNA formats (Table 22). In some instances, an increase in % HbF+ cells was associated with a particular dgRNA form, for example Form C for CR001028 (Table 22). Induction of HbF positive cells by dgRNA including the targeting domain of g8 targeting exon 2 of BCL11A was also observed in parallel. Genomic PCR products of the HPFH region were also subjected to next generation sequencing (NGS) to determine the percentage of edited alleles in the cell population. Genome editing at the HFPH locus was observed in cell cultures electroporated with RNPs containing Cas9, crRNA of the given targeting domain and Tracr (Table 22), but not in control cells with no targeting domain delivered (RNPs containing only Cas9 and Tracr).

Finally, the indel pattern as well as frequency of each indel was assessed for each gRNA by NGS. The most frequently occurring indels at each target site are shown in Table 26.

TABLE 26 5 most frequent indels at each taget sequence after exposure to RNP comprising the indicated gRNA molecule. Each gRNA was tested in dgRNA format in two separate experiments, and the results are shown seperately for each experiment. Capital letters are the naturally occurring nucleotides at and near the target sequence. Deletions relative to the unmodified target sequence are shown as “—”; insertions are shown as lowercase letters. dgRNA Experiment targeting % of all Indel Number domain Variant Read (Genomic Sequence) reads Length 1 CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTCTA- 13.26% −1 ATATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC 1 CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCC------------- 12.48% −13 CCACCGCATCTCTTTCAGCAGTTGTTTC 1 CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTCTA---- 6.04% −4 TCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC 1 CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTCTA-- 3.94% −2 TATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC 1 CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC------------- 3.65% −13 ACCGCATCTCTTTCAGCAGTTGTTTC 1 CR001028 . . . . . . 2 CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCC------------- 14.30% −13 CCACCGCATCTCTTTCAGCAGTTGTTTC 2 CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTCTA- 11.51% −1 ATATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC 2 CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTCTA-- 5.63% −2 TATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC 2 CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTCTA---- 4.98% −4 TCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC 2 CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC------------- 4.91% −13 ACCGCATCTCTTTCAGCAGTTGTTTC 2 CR001028 . . . . . . 1 CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTC------------- 9.10% −13 TTTCAGCAGTTGTTTCTAAAAATATCCTCC 1 CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCCACC- 4.77% −1 CATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC 1 CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCCACC-- 3.54% −2 ATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC 1 CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCCACCGgCATCTCTTTCA 2.51% 1 GCAGTTGTTTCTAAAAATATCCTCC 1 CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCCA----- 2.39% −5 TCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC 1 CR001030 . . . . . . 2 CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTC------------- 9.67% −13 TTTCAGCAGTTGTTTCTAAAAATATCCTCC 2 CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCCACC- 4.87% −1 CATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC 2 CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCCACC-- 3.33% −2 ATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC 2 CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCCACCGgCATCTCTTTCA 2.93% 1 GCAGTTGTTTCTAAAAATATCCTCC 2 CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCCAC- 1.85% −1 GCATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC 2 CR001030 . . . . . . 1 CR001036 CCTAGTTTCATTTTTGCAGAAGTGTTTTAGGCTAAT- 19.08% −1 TAGTGGAATGTATCTTAGAGTTTAACTTATTTGTTTCTGTCAC 1 CR001036 CCTAGTTTCATTTTTGCAGAAGTGTTTTAGGCTAATA-- 17.13% −2 GTGGAATGTATCTTAGAGTTTAACTTATTTGTTTCTGTCAC 1 CR001036 CCTAGTTTCATTTTTGCAGAAGTGTTTTAG---------- 3.55% −10 TGGAATGTATCTTAGAGTTTAACTTATTTGTTTCTGTCAC 1 CR001036 CCTAGTTTCATTTTTGCAGAAGTGTTTTAGGCTAATAaTAGTGGAATGTATCTTAG 2.42% 1 AGTTTAACTTATTTGTTTCTGTCAC 1 CR001036 CCTAGTTTCATTTTTGCAGAAGTGTTTTAGGCTAATA- 2.38% −1 AGTGGAATGTATCTTAGAGTTTAACTTATTTGTTTCTGTCAC 1 CR001036 . . . . . . 2 CR001036 CCTAGTTTCATTTTTGCAGAAGTGTTTTAGGCTAATA-- 22.26% −2 GTGGAATGTATCTTAGAGTTTAACTTATTTGTTTCTGTCAC 2 CR001036 CCTAGTTTCATTTTTGCAGAAGTGTTTTAGGCTAAT- 19.77% −1 TAGTGGAATGTATCTTAGAGTTTAACTTATTTGTTTCTGTCAC 2 CR001036 CCTAGTTTCATTTTTGCAGAAGTGTTTTAG---------- 6.25% −10 TGGAATGTATCTTAGAGTTTAACTTATTTGTTTCTGTCAC 2 CR001036 CCTAGTTTCATTTTTGCAGAAGTGTTTTAGGCTAATA- 1.96% −1 AGTGGAATGTATCTTAGAGTTTAACTTATTTGTTTCTGTCAC 2 CR001036 CCTAGTTTCATTTTTGCAGAAGTGTTTTAGG------------ 1.41% −12 AATGTATCTTAGAGTTTAACTTATTTGTTTCTGTCAC 2 CR001036 . . . . . . 1 CR001043 TAGAGATTTTTGTCTCCAAGGGAATTTTGAGAGGTTG- 5.28% −1 AATGGACAAATCTATTGCTGCAGTTTAAACTTGCTTGCTTCC 1 CR001043 TAGAGATTTTTGTCTCCAAGGGAATTTTGAGAGGTTGGA----- 2.67% −5 CAAATCTATTGCTGCAGTTTAAACTTGCTTGCTTCC 1 CR001043 TAGAGATTTTTGTCTCCAAGGGAATTTTGA--------- 2.62% −9 ATGGACAAATCTATTGCTGCAGTTTAAACTTGCTTGCTTCC 1 CR001043 TAGAGATTTTTGTCTCCAAGGGAATTTTGAGAGG--------- 2.22% −9 ACAAATCTATTGCTGCAGTTTAAACTTGCTTGCTTCC 1 CR001043 TAGAGATTTTTGTCTCCAAGGGAATTTTGAGAGGTTGGgAATGGACAAATCTATTG 2.06% 1 CTGCAGTTTAAACTTGCTTGCTTCC 1 CR001043 . . . . . . 2 CR001043 TAGAGATTTTTGTCTCCAAGGGAATTTTGAGAGGTTG- 5.87% −1 AATGGACAAATCTATTGCTGCAGTTTAAACTTGCTTGCTTCC 2 CR001043 TAGAGATTTTTGTCTCCAAGGGAATTTTGAGAGG--------- 3.11% −9 ACAAATCTATTGCTGCAGTTTAAACTTGCTTGCTTCC 2 CR001043 TAGAGATTTTTGTCTCCAAGGGAATTTTGAGAGGTTGGA----- 2.42% −5 CAAATCTATTGCTGCAGTTTAAACTTGCTTGCTTCC 2 CR001043 TAGAGATTTTTGTCTCCAAGGGAATTTTGAGAGGTTGGgAATGGACAAATCTATTG 1.90% 1 CTGCAGTTTAAACTTGCTTGCTTCC 2 CR001043 TAGAGATTTTTGTCTCCAAGGGAATTTTGA--------- 1.72% −9 ATGGACAAATCTATTGCTGCAGTTTAAACTTGCTTGCTTCC 2 CR001043 . . . . . . 1 CR001080 GAGAAAGGAAGGAAGGAAGAGGGGAAGAGAGAGGATG- 2.72% −1 AAGGGATGGAGGAGAAGAAGGAAAAATAAATAATGGAGAGGA 1 CR001080 GAGAAAGGAAGGAAGGAAGAGGGGAAGAGAGAGGATGGA--------- 2.22% −9 GGAGAAGAAGGAAAAATAAATAATGGAGAGGA 1 CR001080 GAGAAAGGAAGGAAGGAAGAGGGGAAGAGAGAGG-------- 1.44% −8 GATGGAGGAGAAGAAGGAAAAATAAATAATGGAGAGGA 1 CR001080 GAGAAAGGAAGGAAGGAAGAGGGGAAGAGAGAGGATGGgAAGGGATGGAGGAGAAG 1.41% 1 AAGGAAAAATAAATAATGGAGAGGA 1 CR001080 GAGAAAGGAAGGAAGGAAGAGGGGAAGAGAGAGGA---- 1.11% −4 AGGGATGGAGGAGAAGAAGGAAAAATAAATAATGGAGAGGA 1 CR001080 . . . . . . 2 CR001080 GAGAAAGGAAGGAAGGAAGAGGGGAAGAGAGAGGATGGA--------- 3.43% −9 GGAGAAGAAGGAAAAATAAATAATGGAGAGGA 2 CR001080 GAGAAAGGAAGGAAGGAAGAGGGGAAGAGAGAGGATG- 3.17% −1 AAGGGATGGAGGAGAAGAAGGAAAAATAAATAATGGAGAGGA 2 CR001080 GAGAAAGGAAGGAAGGAAGAGGGGAAGAGA--------- 1.61% −9 AGGGATGGAGGAGAAGAAGGAAAAATAAATAATGGAGAGGA 2 CR001080 GAGAAAGGAAGGAAGGAAGAGGGGAAGAGAGAGGA---- 1.28% −4 AGGGATGGAGGAGAAGAAGGAAAAATAAATAATGGAGAGGA 2 CR001080 GAGAAAGGAAGGAAGGAAGAGGGGAAGAGAGAGG-------- 1.16% −8 GATGGAGGAGAAGAAGGAAAAATAAATAATGGAGAGGA 2 CR001080 . . . . . . 1 CR001095 GAGAAAGAGAAAGGGAAGGGAAGAGAGGAAAGAAGA-- 5.94% −2 AGAGGAGAGAAAAGAAACGAAGAGAGGGGAAGGGAAGGAAAA 1 CR001095 GAGAAAGAGAAAGGGAAGGGAAGAGAGGAAAGAAGAG----- 5.54% −5 GAGAGAAAAGAAACGAAGAGAGGGGAAGGGAAGGAAAA 1 CR001095 GAGAAAGAGAAAGGGAAGGGAAGAGAGGA--------------- 4.02% −15 GAGAAAAGAAACGAAGAGAGGGGAAGGGAAGGAAAA 1 CR001095 GAGAAAGAGAAAGGGAAGGGAAGAGAGGAAAGAA-------------------- 3.23% −20 ACGAAGAGAGGGGAAGGGAAGGAAAA 1 CR001095 GAGAAAGAGAAAGGGAAGGGAAGAGAGGAAAGA-------- 2.49% −8 GGAGAGAAAAGAAACGAAGAGAGGGGAAGGGAAGGAAAA 1 CR001095 . . . . . . 2 CR001095 GAGAAAGAGAAAGGGAAGGGAAGAGAGGAAAGAAGAG----- 7.89% −5 GAGAGAAAAGAAACGAAGAGAGGGGAAGGGAAGGAAAA 2 CR001095 GAGAAAGAGAAAGGGAAGGGAAGAGAGGAAAGAAGA-- 6.18% −2 AGAGGAGAGAAAAGAAACGAAGAGAGGGGAAGGGAAGGAAAA 2 CR001095 GAGAAAGAGAAAGGGAAGGGAAGAGAGGA--------------- 4.16% −15 GAGAAAAGAAACGAAGAGAGGGGAAGGGAAGGAAAA 2 CR001095 GAGAAAGAGAAAGGGAAGGGAAGAGAGGAAAGAAGAGgAAGAGGAGAGAAAAGAAA 2.77% 1 CGAAGAGAGGGGAAGGGAAGGAAAA 2 CR001095 GAGAAAGAGAAAGGGAAGGGA-------------------- 1.98% −20 GGAGAGAAAAGAAACGAAGAGAGGGGAAGGGAAGGAAAA 2 CR001095 . . . . . . 1 CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC------- 6.73% −7 ACTTAAATGCTTACCAACAGTAGAATTGATAAAT 1 CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACCGGTAGgCCACTTAAATG 4.02% 1 CTTACCAACAGTAGAATTGATAAAT 1 CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACCGGTAaGCCACTTAAATG 2.87% 1 CTTACCAACAGTAGAATTGATAAAT 1 CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCA-------- 1.71% −8 GCCACTTAAATGCTTACCAACAGTAGAATTGATAAAT 1 CR001137 AAATGCTTATGACAGCAATAATCATAAAAACC-------------- 0.95% −14 ACTTAAATGCTTACCAACAGTAGAATTGATAAAT 1 CR001137 . . . . . . 2 CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC------- 7.25% −7 ACTTAAATGCTTACCAACAGTAGAATTGATAAAT 2 CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACCGGTAGgCCACTTAAATG 3.44% 1 CTTACCAACAGTAGAATTGATAAAT 2 CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACCGGTAaGCCACTTAAATG 2.50% 1 CTTACCAACAGTAGAATTGATAAAT 2 CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACCGGTA-------- 1.37% −8 AATGCTTACCAACAGTAGAATTGATAAAT 2 CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACCGGT------- 1.11% −7 TAAATGCTTACCAACAGTAGAATTGATAAAT 2 CR001137 . . . . . . 1 CR001142 AAATGCATTTTACAGCATTTGGTTGATTAAAAGTAACCcAGAGGTGAGTTCAAACT 8.00% 1 ATATGACTTTATTTGTATATAGAAA 1 CR001142 AAATGCATTTTACAGCATTTGGTTGATTAAAAG------- 6.63% −7 AGGTGAGTTCAAACTATATGACTTTATTTGTATATAGAAA 1 CR001142 AAATGCATTTTACAGCATTTGGTTGATTAAAAGTAAC- 2.86% −1 AGAGGTGAGTTCAAACTATATGACTTTATTTGTATATAGAAA 1 CR001142 AAATGCATTTTACAGCATTTGGTTGATTAAAAG--------- 2.03% −9 GTGAGTTCAAACTATATGACTTTATTTGTATATAGAAA 1 CR001142 AAATGCATTTTACAGCATTTGGTTGA-------------------- 1.71% −20 GTTCAAACTATATGACTTTATTTGTATATAGAAA 1 CR001142 . . . . . . 2 CR001142 AAATGCATTTTACAGCATTTGGTTGATTAAAAGTAACCcAGAGGTGAGTTCAAACT 9.94% 1 ATATGACTTTATTTGTATATAGAAA 2 CR001142 AAATGCATTTTACAGCATTTGGTTGATTAAAAG------- 5.81% −7 AGGTGAGTTCAAACTATATGACTTTATTTGTATATAGAAA 2 CR001142 AAATGCATTTTACAGCATTTGGTTGATTAAAAGTAAC- 4.19% −1 AGAGGTGAGTTCAAACTATATGACTTTATTTGTATATAGAAA 2 CR001142 AAATGCATTTTACAGCATTTGGTTGATTAAAAG--------- 2.59% −9 GTGAGTTCAAACTATATGACTTTATTTGTATATAGAAA 2 CR001142 AAATGCATTTTACAGCATTTGGTTGA-------------------- 2.26% −20 GTTCAAACTATATGACTTTATTTGTATATAGAAA 2 CR001142 . . . . . . 1 CR001158 CCTGGAAGCCAACGAAAGATATTGAATAATTCAAGAAAaGGTGGTGGCATGGTTTG 10.94% 1 ATTTGTGTCTTTAAAAGATTATTCT 1 CR001158 CCTGGAAGCCAACGAAAGATATTGAATAATTCAAG---- 10.03% −4 GTGGTGGCATGGTTTGATTTGTGTCTTTAAAAGATTATTCT 1 CR001158 CCTGGAAGCCAACGAAAGATATTGAATAATTCAAGAA- 3.80% −1 GGTGGTGGCATGGTTTGATTTGTGTCTTTAAAAGATTATTCT 1 CR001158 CCTGGAAGCCAACGAAAGATATTGAATAATTCAAGA-- 1.19% −2 GGTGGTGGCATGGTTTGATTTGTGTCTTTAAAAGATTATTCT 1 CR001158 CCTGGAAGCCAACGAAAGATATTGAATAATTCA----- 0.78% −5 GGTGGTGGCATGGTTTGATTTGTGTCTTTAAAAGATTATTCT 1 CR001158 . . . . . . 2 CR001158 CCTGGAAGCCAACGAAAGATATTGAATAATTCAAGAAAaGGTGGTGGCATGGTTTG 11.89% 1 ATTTGTGTCTTTAAAAGATTATTCT 2 CR001158 CCTGGAAGCCAACGAAAGATATTGAATAATTCAAG---- 9.97% −4 GTGGTGGCATGGTTTGATTTGTGTCTTTAAAAGATTATTCT 2 CR001158 CCTGGAAGCCAACGAAAGATATTGAATAATTCAAGAA- 3.45% −1 GGTGGTGGCATGGTTTGATTTGTGTCTTTAAAAGATTATTCT 2 CR001158 CCTGGAAGCCAACGAAAGATATTGAATAATTCAAGA-- 0.86% −2 GGTGGTGGCATGGTTTGATTTGTGTCTTTAAAAGATTATTCT 2 CR001158 CCTGGAAGCCAACGAAAGATATTGAATAATTCAAGAAcaAGGTGGTGGCATGGTTT 0.49% 2 GATTTGTGTCTTTAAAAGATTATTCT 2 CR001158 . . . . . . 1 CR001212 CCTTGGCCTCCCAAAGTGCTGGGTTTACAAGCCTGAGCCA------------- 11.38% −13 GGATAAGGTCTAAAAGTGGAAAGAATA 1 CR001212 CCTTGGCCTCCCAAAGTGCTGGGTTTACAAGCCTGAGCCACC- 3.98% −1 CATCCAGCCAGGATAAGGTCTAAAAGTGGAAAGAATA 1 CR001212 CCTTGGCCTCCCAAAGTGCTGGGTTTACAAGCCTGAGCCA----- 3.05% −5 TCCAGCCAGGATAAGGTCTAAAAGTGGAAAGAATA 1 CR001212 CCTTGGCCTCCCAAAGTGCTGGGTTTACAAGCCTGAGCCACCG- 2.94% −1 ATCCAGCCAGGATAAGGTCTAAAAGTGGAAAGAATA 1 CR001212 CCTTGGCCTCCCAAAGTGCTGGGTTTACAAGCCTGAGCCACC------ 2.82% −6 AGCCAGGATAAGGTCTAAAAGTGGAAAGAATA 1 CR001212 . . . . . . 2 CR001212 CCTTGGCCTCCCAAAGTGCTGGGTTTACAAGCCTGAGCCA------------- 11.42% −13 GGATAAGGTCTAAAAGTGGAAAGAATA 2 CR001212 CCTTGGCCTCCCAAAGTGCTGGGTTTACAAGCCTGAGCCACC- 6.41% −1 CATCCAGCCAGGATAAGGTCTAAAAGTGGAAAGAATA 2 CR001212 CCTTGGCCTCCCAAAGTGCTGGGTTTACAAGCCTGAGCCACCG- 5.61% −1 ATCCAGCCAGGATAAGGTCTAAAAGTGGAAAGAATA 2 CR001212 CCTTGGCCTCCCAAAGTGCTGGGTTTACAAGCCTGAGCCACCG-- 2.85% −2 TCCAGCCAGGATAAGGTCTAAAAGTGGAAAGAATA 2 CR001212 CCTTGGCCTCCCAAAGTGCTGGGTTTACAAGCCTGAGCCACC------ 1.96% −6 AGCCAGGATAAGGTCTAAAAGTGGAAAGAATA 2 CR001212 . . . . . . 1 CR001217 AAGTGCTGGGTTTACAAGCCTGAGCCACCGCATCCAGCCAGG------ 17.75% −6 TCTAAAAGTGGAAAGAATAGCATCTACTCTTG 1 CR001217 AAGTGCTGGGTTTACAAGCCTGAGCCACCGCATCCAGCCAGGATtAAGGTCTAAAA 4.06% 1 GTGGAAAGAATAGCATCTACTCTTG 1 CR001217 AAGTGCTGGGTTTACAAGCCTGAGCCACCGCATCCAGCCAGGAaTAAGGTCTAAAA 2.38% 1 GTGGAAAGAATAGCATCTACTCTTG 1 CR001217 AAGTGCTGGGTTTACAAGCCTGAGCCACCGCATCCAGCCAGGA- 1.35% −1 AAGGTCTAAAAGTGGAAAGAATAGCATCTACTCTTG 1 CR001217 AAGTGCTGGGTTTACAAGCCTGAGCCACCGCATCCAGCCAGGAT----- 1.10% −5 CTAAAAGTGGAAAGAATAGCATCTACTCTTG 1 CR001217 . . . . . . 2 CR001217 AAGTGCTGGGTTTACAAGCCTGAGCCACCGCATCCAGCCAGG------ 18.91% −6 TCTAAAAGTGGAAAGAATAGCATCTACTCTTG 2 CR001217 AAGTGCTGGGTTTACAAGCCTGAGCCACCGCATCCAGCCAGGATtAAGGTCTAAAA 5.59% 1 GTGGAAAGAATAGCATCTACTCTTG 2 CR001217 AAGTGCTGGGTTTACAAGCCTGAGCCACCGCATCCAGCCAGGAaTAAGGTCTAAAA 1.42% 1 GTGGAAAGAATAGCATCTACTCTTG 2 CR001217 AAGTGCTGGGTTTACAAGCCTGAGCCACCGCATCCAGCCAGGA- 1.38% −1 AAGGTCTAAAAGTGGAAAGAATAGCATCTACTCTTG 2 CR001217 AAGTGCTGGGTTTACAAGCCTGAGCCACCGCATCCAGCCAGGAT----- 1.26% −5 CTAAAAGTGGAAAGAATAGCATCTACTCTTG 2 CR001217 . . . . . . 1 CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCTG---- 28.78% −4 GGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA 1 CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCT- 9.51% −1 ACTGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA 1 CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGGAC----- 4.35% −5 TGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA 1 CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGG----------- 1.87% −11 CAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA 1 CR001221 TAGCATCTACTCTTGTTCAGGAAACAATG------------ 1.71% −12 GGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA 1 CR001221 . . . . . . 2 CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCTG---- 29.12% −4 GGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA 2 CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCT- 10.32% −1 ACTGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA 2 CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGGAC----- 4.26% −5 TGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA 2 CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGGAC---------- 1.89% −10 AGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA 2 CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGG----------- 1.67% −11 CAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA 2 CR001221 . . . . . .

Although in some cases, the relative abundance of the most frequent indels varied from experiment to experiment, the top indels were largely the same across both experiments for any given gRNA. This indicates that for these dgRNAs, the indel pattern created in HSC cells was consistent. As well, these results support the surprising finding from earlier experiments that small indels (e.g., in this case, indels from 1-20 nucleotides) in the HPFH regions targeted by these gRNAs could result in significant upregulation of fetal hemoglobin. An increase in HbF-containing erythrocytes derived from genome edited cells is likely to have therapeutic implications by reduced sickling.

Example 4.5

Methods: Methods are as in Sub-Example 4.1, with the Following Exceptions.

Human CD34⁺ cell culture. Human CD34+ cells were derived from bone marrow (Hemacare Corporation, Cat. No. BM34C-3). CD34+ cells were thawed and expanded in expansion medium for 1 day prior to RNP delivery. After RNP delivery, cells were immediately transferred back into 200 μl expansion medium and allowed to recover overnight. The following day, the cultures were counted and adjusted to 2.0×10⁵ viable cells per ml. Percent recovery was calculated as the viable cell count 1 day after RNP delivery as a percentage of the viable cells electroporated. After an additional 7 days in expansion medium (8 days following RNP delivery), the viable cell count was again determined. Fold proliferation was calculated as the viable cell count after 7 days in expansion medium divided by 2.0×10⁵ cells per ml. All viable cell counts were measured by flow cytometry using AccuCheck Counting Beads (ThermoFisher cat. No. PCB100) with inviable cells discriminated by DAPI (4′,6-Diamidino-2-Phenylindole) staining After an additional 1 day in expansion medium (9 days following RNP delivery), the cell cultures were phenotyped by flow cytometry as described under Cell phenotyping.

Assembly of Cas9 and guide RNA ribonucleoprotein (RNP) complexes, preparation of HSPC, and electroporation of RNP into HSPC. The HSPC collected by centrifugation were resuspended in P3 Primary Cell Solution (Lonza cat. No. PBP3-00675) at a cell density of 5.4×10⁶/mL. The RNP was mixed with 20 μL of cells by pipetting up and down and incubated at RT for 2 min. The RNP/cell mixture (20 μL) was electroporated using code CM-137 on the 4D-Nucleofector (Lonza). Electroporations were performed in duplicate. The crRNAs used were of the sequence mN*mN*mN*rNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrGrUrUrUrUrArGrArGrCrUrArU*mG*m C*mU, where r indicates an RNA base, m indicates a base with 2′O-Methyl modification, and * indicates a Phosphorothioate Bond. N's indicate the residues of the indicated targeting domain. The tracr sequence used was SEQ ID NO: 7808.

Colony forming unit cell assay. The day following RNP delivery, viable cells were counted as described in Human CD34+ cell culture. For the granulocyte/macrophage progenitor colony forming unit (CFU) assay, 227 cells per 1 mL Methocult H4035 methylcellulose medium (StemCell Technologies) was plated in duplicate. 1× antibiotic/antimycotic (Gibco, Cat. #10378-016) was added into the Methocult. The culture dishes were incubated in a humidified incubator at 37° C. Colonies containing at least 50 cells were counted at day 15 post-plating. Colony number per ml of Methocult was divided by 227 and multiplied by 1000 to obtain the CFU frequency per 1000 cells.

Cell phenotyping. Cells were analyzed for surface marker expression after staining with the following antibody panels. Panel 1: Antibodies specific for CD38 (FITC-conjugate, BD Biosciences #340926, clone HB7), CD133 epitope 1 (PE-conjugate, Miltenyi #130-080-801, clone AC133), CD34 (PerCP-conjugate, BD Biosciences #340666, clone 8G12), CD90 (APC-conjugate, BD Biosciences #598695, clone E10), CD45RA (Pe-Cy7-conjugate, eBioscience #25-0458-42, clone HI100). Panel 2: CD34 (PerCP-conjugate, BD Biosciences #340666, clone 8G12), CD33 (PE-Cy7-conjugate, BD Biosciences #333946, clone P67.6), CD14 (APC-H7-conjugate, BD Biosciences #560270, clone MφP9), CD15 (PE-conjugate, Biolegend #301905, clone HI98). Panel 3: CD34 (PerCP-conjugate, BD Biosciences #340666, clone 8G12), CD41a (APC-H7-conjugate, BD Biosciences #561422, clone HIPS), CD71 (FITC-conjugate, BD Biosciences #555536, clone M-A712), CD19 (PE-conjugate, BD Biosciences #340720, clone SJ25C1), CD56 (APC-conjugate, Biolegend #318310, clone HCD56). Corresponding isotype control antibody panels were used to stain cultures in parallel, except that anti-CD45RA was included instead of its isotype control. Inviable cells were discriminated by DAPI (4′,6-Diamidino-2-Phenylindole) staining Stained samples were analyzed on an LSRFortessa flow cytometer (BD Biosciences) for cell surface protein expression. The results were analyzed using Flowjo, and data were presented as % of the DAPI negative viable cell population.

Genomic DNA preparation and next generation sequencing (NGS). Genomic DNA was prepared from edited and unedited HSPC at 1 and 8 days post-electroporation using Quick Extract DNA Extraction Solution (Epicentre Cat # QE09050).

Results:

Without being bound by theory, it is believed that targeted genetic disruption of the HPFH or BCL11A erythroid enhancer region will relieve repression of γ-globin expression, allowing production of the red blood cells containing elevated HbF protein, (cells expressing fetal hemoglobin are sometimes referred to herein as “F-cells”). The elevated HbF prevents sickling of the red blood cells under deoxygenated conditions and will be therapeutic/curative for the patients of both β-thalassemia and SCD. Autologous hematopoietic stem cell transplantation (HSCT) with ex vivo genome edited HSC from SCD patients was also combined with stem cell expansion enhancing technology, e.g., an aryl hydrocarbon receptor (AHR) inhibitor, e.g., as described in WO2010/059401 (the contents of which are incorporated by reference in their entirety), e.g., Compound 4 to improve ex vivo expansion and increase the dose of gene modified HSC delivered.

For efficient genome editing via programmable nuclease, Cas9, the successful delivery of guide RNA (gRNA) and Cas9 protein into target cells and tissues is essential. Recent reports demonstrated that Cas9 ribonucleoprotein (RNP) complexes when delivered into target cells by electroporation can accomplish efficient and specific genome editing in several different cell types. Cas9-RNP complexes cleave chromosomal DNA almost immediately after delivery and are degraded rapidly in cells, reducing off-target effects. In contrast, use of plasmid and viral vector systems used to deliver Cas9 results in prolonged expression of the enzyme aggravating off-target effects associated with the system. Additionally, delivery of RNPs into the target cells requires no additional tools which would greatly facilitate translation of genome editing for therapeutic purposes in the clinic. Purified recombinant Cas9 protein and gRNA complexes (RNPs) were delivered into cultured HSPC and an overview experiments used are shown in FIG. 17.

Recombinant Cas9 protein was purified from Escherichia coli and complexed with synthetic dual gRNAs (dgRNA) that consist of crRNA and tracr to generate ribonucleoprotein (RNP) complexes. The list of gRNAs used in the study are shown in Table 23. The RNP complexes were electroporated into CD34+ HSPC via electroporation as described under materials and methods. The cells were expanded prior to the delivery of RNP complexes. Actively dividing cells may facilitate uptake of RNP complexes delivered by electroporation.

TABLE 23 Relative viable cell recovery, proliferation in CD34+ medium, and granulocyte/macrophage progenitor colony forming unit (CFU) frequency for edited and unedited cell cultures in the current study. Percent recovery, Fold proliferation and CFU frequency were calculated as described in Materials and Methods. Individual electroporation replicates are shown. All gRNA molecules were tested in the dgRNA format. The Tracr sequence was SEQ ID NO: 7808, and the crRNA had the following format with 2′O-Methyl (m) and Phosphorothioate Bond (*) modifications indicated: mN*mN*mN*rNrNrNrNrNrNrNrNrNrNrNrNr NrNrNrNrNrGrUrUrUrUrArGrArGrCrUrArU*mG*m C*mU, where N's are the residues of the indicated targeting domain Fold Guide RNA targeting % proliferation CFU (per domain ID and replicate recovery (7 days) 1000 cells) CR001030 replicate 1 77.7 7.1 117 CR001030 replicate 2 87.9 4.8 95 CR001028 replicate 1 85.3 10.6 176 CR001028 replicate 2 82.1 10.9 141 CR001095 replicate 1 72.5 7.3 121 CR001095 replicate 2 73.3 7.3 126 CR001212 replicate 1 75.6 7.7 123 CR001212 replicate 2 75.5 8.2 97 CR000312 replicate 1 77.7 12.2 145 CR000312 replicate 2 81.0 9.0 143 g8 replicate 1 80.0 16.6 145 g8 replicate 2 84.6 17.3 145 None/control replicate 1 89.8 19.3 185 None/control replicate 2 81.2 20.5 154

Percent cell recovery at 1 day after electroporation ranged from 72.5% to 89.8% and was similar across conditions, including the unedited but electroporated control (Table 23). The genome edited and unedited HSPC were analyzed for proliferation in CD34+ cell expansion medium. Proliferation ranged from 4.8-fold to 17.3-fold over 7 days for edited cell cultures, and ranged from 19.3 to 20.5-fold for unedited cells (Table 22). Editing by dgRNAs in this study targeting the HPFH or BCL11A erythroid enhancer regions did not alter the composition of cell types in the culture compared to unedited control, as determined by surface marker expression, indicating that targeting these sites does not alter HSPC fate under these conditions (FIG. 26A-B). In contrast, editing with dgRNA targeting g8 in the BCL11A exon resulted in a modest reduction in proliferation but a marked shift in cell composition, specifically a decrease in the percentage of all CD34+ HSPC sub-types as well as of the CD71+ erythroid population and an increase in the percentage of CD14+ monocyte and CD15+ granulocyte populations (Table 23 and FIG. 26A-B). The frequency of granulocyte/macrophage progenitor colony forming units (CFU) was similar across edited cultures, with only a modest CFU reduction in edited cultures (ranging from 95 to 145 CFU per 1000 cells) compared with unedited cultures (154 to 185 CFU per 1000 cells), suggesting that granulocyte/macrophage progenitor function is not grossly altered by targeting these sites (Table 23).

Example 4.6

Methods: Methods are as in Example 4, with the Following Exceptions.

Assembly of Cas9 and guide RNA ribonucleoprotein (RNP) complexes, preparation of HSPC, and electroporation of RNP into HSPC. In some instances, crRNAs containing two different targeting domains were delivered into the same cell culture. In these instances, the total RNP delivered to cells contained 6 μg of Cas9, 3 μg of crRNA and 3 μg of Tracr, as in sub-example 4.1; however, the two crRNAs containing 1.5 μg each were independently complexed Tracr/CAS9 mixtures containing 1.5 μg Tracr and 3 μg Cas9 and only combined when added to the cells. The HSPC collected by centrifugation were resuspended in P3 Primary Cell Solution (Lonza cat. No. PBP3-00675) at a cell density of 2.5×10⁶/mL. The RNP was mixed with 20 μL of cells by pipetting up and down and incubated at RT for 2 min. The RNP/cell mixture (20 μL) was electroporated using code CM-137 on the 4D-Nucleofector (Lonza). Electroporations were performed in duplicate. The dgRNA format used a tracr having SEQ ID NO: 7808, and a crRNA of the sequence mN*mN*mN*rNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrGrUrUrUrUrArGrArGrCrUrArU*mG*m C*mU, where r indicates an RNA base, m indicates a base with 20-Methyl modification, and * indicates a Phosphorothioate Bond, and N's indicate the residues of the indicated targeting domain.

In vitro erythropoiesis and FACS analysis for HbF containing erythroid cells. The cell culture was diluted in fresh medium after 3 days.

Genomic DNA preparation and next generation sequencing (NGS). Genomic DNA was prepared from edited and unedited HSPC at 3 days post-electroporation using Quick Extract DNA Extraction Solution (Epicentre Cat # QE09050).

Results:

Without being bound by theory, it is believed that targeted genetic disruption of the HPFH or BCL11A erythroid enhancer region will relieve repression of γ-globin expression, allowing production of the red blood cells containing elevated HbF protein, (cells expressing fetal hemoglobin are sometimes referred to herein as “F-cells”). The elevated HbF prevents sickling of the red blood cells under deoxygenated conditions and will be therapeutic/curative for the patients of both β-thalassemia and SCD. Autologous hematopoietic stem cell transplantation (HSCT) with ex vivo genome edited HSC from SCD patients was also combined with stem cell expansion enhancing technology, e.g., an aryl hydrocarbon receptor (AHR) inhibitor, e.g., as described in WO2010/059401 (the contents of which are incorporated by reference in their entirety), e.g., Compound 4 to improve ex vivo expansion and increase the dose of gene modified HSC delivered.

For efficient genome editing via programmable nuclease, Cas9, the successful delivery of guide RNA (gRNA) and Cas9 protein into target cells and tissues is essential. Recent reports demonstrated that Cas9 ribonucleoprotein (RNP) complexes when delivered into target cells by electroporation can accomplish efficient and specific genome editing in several different cell types. Cas9-RNP complexes cleave chromosomal DNA almost immediately after delivery and are degraded rapidly in cells, reducing off-target effects. In contrast, use of plasmid and viral vector systems used to deliver Cas9 results in prolonged expression of the enzyme aggravating off-target effects associated with the system. Additionally, delivery of RNPs into the target cells requires no additional tools which would greatly facilitate translation of genome editing for therapeutic purposes in the clinic. Purified recombinant Cas9 protein and gRNA complexes (RNPs) were delivered into cultured HSPC and an overview experiments used are shown in FIG. 17.

Recombinant Cas9 protein was purified from Escherichia coli and complexed with synthetic dual gRNAs (dgRNA) that consist of crRNA and tracr to generate ribonucleoprotein (RNP) complexes. The list of gRNAs used in the study are shown in Table 24. The RNP complexes were electroporated into CD34+ HSPC via electroporation as described under materials and methods. The cells were expanded prior to the delivery of RNP complexes. Actively dividing cells may facilitate uptake of RNP complexes delivered by electroporation.

TABLE 24 HbF induction by simultaneous targeting of both the BCL11A erythroid enhancer and HPFH regions. All gRNA molecules were tested in the dgRNA format in duplicate. The tracr used has the sequence of SEQ ID NO: 7808, and the crRNA had the following format with 2′O-Methyl (m) and Phosphorothioate Bond (*) modifications indicated: mN*mN*mN*rNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrNrGrUrUrUrUr ArGrArGrCrUrArU*mG*mC*mU, where N's are the residues of the indicated targeting domain. Guide % edited at % edited at RNA % HbF+ targeting targeting Guide RNA targeting (F cells), site #1, site #2, targeting domain domain average of average of average of ID #1 ID #2 replicates replicates replicates CR000312 n/a 41.3 91.3 n/a CR001128_EH15 n/a 43.7 77.5 n/a n/a CR001030 58.0 n/a 85.6 n/a CR001221 48.6 n/a 92.1 CR000312 CR001030 66.8 58.3 81.2 CR000312 CR001221 60.6 64.2 85.0 CR001128_EH15 CR001030 69.1 49.8 82.9 CR001128_EH15 CR001221 62.7 58.5 84.8 g8 n/a 64.7 94.6 n/a None/control n/a 23.8 n/a n/a

The genome edited and unedited HSPC were analyzed by flow cytometry for expression levels of fetal globin and two erythroid cell surface markers, transferrin receptor (CD71) and glycophorin A (CD235a) using antibodies conjugated to fluorescent dyes. The live cells were identified and gated by exclusion of Live Dead Violet. HPFH region or BCL11A erythroid enhancer targeting resulted in increased percentage of erythroid cells containing HbF compared to mock electroporated cells (Table 24). Induction of HbF positive cells by dgRNA including the targeting domain of g8 targeting exon 2 of BCL11A was also observed in parallel. When the HPFH region and BCL11A erythroid enhancer were targeted simultaneously in the same cell population, the percentage of HbF containing cells was increased beyond that of targeting either region independently (Table 24). Thus, an increase in HbF-containing erythrocytes derived from edited cells can be achieved by targeting either the HPFH region or BCL erythroid enhancer, as well as to a greater extent by simultaneous targeting of both regions.

Genomic PCR products of both regions were independently subjected to next generation sequencing (NGS) to determine the percentage of edited alleles in the cell population. Genome editing was observed in cell cultures electroporated with RNPs containing Cas9, crRNA of the given targeting domain and Tracr (Table 24), but not in control cells with no targeting domain delivered (RNPs containing only Cas9 and Tracr). When RNPs targeting two sites were delivered into the same cell population, editing at both sites was observed (Table 24). In some instances, the percent edited cells at a given site was modestly reduced when two RNPs were delivered compared with when only one RNP was delivered (Table 24), possibly due to the lower RNP concentration targeting a given site in the former instance. Higher editing percentages and potentially higher percentages of HbF containing cells may be achieved by increasing the each individual RNP concentration when two RNPs are delivered simultaneously. An increase in HbF-containing erythrocytes derived from genome edited cells is likely to have therapeutic implications by reduced sickling.

Example 4.7

Methods: Methods are as in Example 4, with the Following Exceptions.

Human CD34+ cell culture. Human CD34+ cells were derived from bone marrow (Lonza, Cat. No. 2M-101D). CD34+ cells were thawed and expanded for 2 days in expansion medium prior to RNP delivery.

Assembly of Cas9 and guide RNA ribonucleoprotein (RNP) complexes, preparation of HSPC, and electroporation of RNP into HSPC. For formation of RNP using single guide RNAs (sgRNAs), 6 μg of sgRNA was added to 6 μg of CAS9 protein (in 0.8 to 1 μL) and 0.5 μL of 5×CCE buffer (20 mM HEPES, 100 mM KCL, 5 mM MgCL2, 5% Glycerol and freshly added 1 mM DTT) in a total volume of 5 μL and incubated for 5 min at 37° C. The HSPC were collected by centrifugation were resuspended in P3 Primary Cell Solution (Lonza cat. No. PBP3-00675) at a cell density of 6.4×106/mL. The RNP was mixed with 20 μL of cells by pipetting up and down and incubated at RT for 2 min. The RNP/cell mixture (20 μL) was electroporated using code CM-137 on the 4D-Nucleofector (Lonza). Electroporations were performed in duplicate. For dgRNA, dgRNA-PS and dgRNA-OMePS the Tracr was SEQ ID NO: 6660, with the exception of g8 which was used with Tracr SEQ ID NO: 7808. The formats for all gRNAs used in this experiment are shown in Table 36, with the exception of the dgRNA g8 OMePS, which included a crRNA having the sequence mC*mA*mC*AAACGGAAACAAUGCAAGUUUUAGAGCUAU*mG*mC*mU. and a tracr having the sequence of SEQ ID NO: 7808.

In vitro erythropoiesis and FACS analysis for HbF containing erythroid cells. After RNP delivery, cells were maintained as per Protocol 1 or Protocol 2. For Protocol 1, the cells were immediately transferred into pre-warmed medium consisting of EDM and supplements. During days 0-7 of culture, EDM was further supplemented with 1 μM hydrocortisone (Sigma H8672), 100 ng/mL human SCF (Life Technologies, Cat. #PHC2113), and 5 ng/mL human IL-3 (Peprotech #10779-598). During days 7-11 of culture, EDM was supplemented with 100 ng/mL of human SCF only. During days 11-21 of culture, EDM had no additional supplements. Cell cultures were adjusted to 4.0×10⁴ cells per ml on day 7. On days 11, 14 and 19, the media was replenished. For Protocol 2, cells were immediately transferred back into 200 al expansion medium and allowed to expand for an additional 2 days. The cultures were counted at 2 days after RNP delivery. The cells were then pelleted and resuspended in pre-warmed medium consisting of EDM and supplements. During days 0-7 of EDM culture, EDM was further supplemented with 1 μM hydrocortisone (Sigma H8672), 100 ng/mL human SCF (Life Technologies, Cat. #PHC2113), and 5 ng/mL human IL-3 (Peprotech #10779-598). During days 7-11 of culture, EDM was supplemented with 100 ng/mL of human SCF only. During days 11-21 of culture, EDM had no additional supplements. Cell cultures were initiated at 4.0×10⁴ cells per ml on day 0, diluted 4-fold with fresh medium on day 4, and adjusted to 2.0×10⁵ cells per ml on day 7. On days 11, 14 and 19, the media was replenished. Viable cells were counted at 7, 18 and 21 days in EDM culture. All viable cell counts were determined by flow cytometry using AccuCheck Counting Beads (ThermoFisher cat. No. PCB100) with inviable cells discriminated by DAPI (4′,6-Diamidino-2-Phenylindole) staining. For both protocols, on days 7, 14 and 21 of the erythroid differentiation culture, the cells were analyzed by intracellular staining for HbF expression. On days 14 and 21 intracellular staining for HbF expression did not include anti-CD71 and anti-CD235a antibodies, and % of HbF positive cells (F-cells) in the entire viable cell population was reported. LIVE/DEAD® Fixable Near-IR Dead Cell Stain (ThermoFisher L34975) was used as the viability dye.

Genomic DNA preparation and next generation sequencing (NGS). Genomic DNA was prepared at 2 and 6 days post-electroporation from edited and unedited HSPC cultured by Protocol 2 using Quick Extract DNA Extraction Solution (Epicentre Cat # QE09050).

Results:

Without being bound by theory, it is believed that targeted genetic disruption of the HPFH region will relieve repression of γ-globin expression, allowing production of the red blood cells containing elevated HbF protein, (cells expressing fetal hemoglobin are sometimes referred to herein as “F-cells”). The elevated HbF prevents sickling of the red blood cells under deoxygenated conditions and will be therapeutic/curative for the patients of both β-thalassemia and SCD. Autologous hematopoietic stem cell transplantation (HSCT) with ex vivo genome edited HSC from SCD patients was also combined with stem cell expansion enhancing technology, e.g., an aryl hydrocarbon receptor (AHR) inhibitor, e.g., as described in WO2010/059401 (the contents of which are incorporated by reference in their entirety), e.g., Compound 4 to improve ex vivo expansion and increase the dose of gene modified HSC delivered.

For efficient genome editing via programmable nuclease, Cas9, the successful delivery of guide RNA (gRNA) and Cas9 protein into target cells and tissues is essential. Recent reports demonstrated that Cas9 ribonucleoprotein (RNP) complexes when delivered into target cells by electroporation can accomplish efficient and specific genome editing in several different cell types. Cas9-RNP complexes cleave chromosomal DNA almost immediately after delivery and are degraded rapidly in cells, reducing off-target effects. In contrast, use of plasmid and viral vector systems used to deliver Cas9 results in prolonged expression of the enzyme aggravating off-target effects associated with the system. Additionally, delivery of RNPs into the target cells requires no additional tools which would greatly facilitate translation of genome editing for therapeutic purposes in the clinic. Purified recombinant Cas9 protein and gRNA complexes (RNPs) were delivered into cultured HSPC and an overview experiments used are shown in FIG. 17.

Recombinant Cas9 protein was purified from Escherichia coli and complexed with synthetic single gRNAs (sgRNA) or dual gRNAs (dgRNA) that consist of crRNA and tracr to generate ribonucleoprotein (RNP) complexes. The formats of gRNAs used in the study are shown in Table 36. The RNP complexes were electroporated into CD34+ HSPC via electroporation as described under materials and methods. The cells were expanded prior to the delivery of RNP complexes and, in some cases (Protocol 2) also after electroporation. Actively dividing cells may facilitate uptake of RNP complexes delivered by electroporation.

Genomic PCR products of the HPFH region were subjected to next generation sequencing (NGS) to determine the percentage of edited alleles in the cell population. Genome editing at the HFPH locus was observed in cell cultures electroporated with RNPs containing Cas9, crRNA of the given targeting domain and Tracr (FIG. 43), but not in control cells with no targeting domain delivered (RNPs containing only Cas9 and Tracr). In some instances, editing was greater at a given target site using modified sgRNAs relative to the other gRNA formats (FIG. 43). Finally, the indel pattern as well as frequency of each indel was assessed for each gRNA by NGS. Indel pattern across multiple replicates using the same gRNA/Cas9 were similar Representative most frequently occurring indels at each target site are shown in Table 37.

TABLE 36 gRNA sequences used in the experiments described in this sub-example. N indicates the residues of the indicated targeting domain; mN indicates a 2′-OMe-modified nucleic acid; *indicates a phosphorothioate modification. Label Format Sequence CRxxxxxx sgRNA NNNNNNNNNNNNNNNNNNNNGUUUUAGAGCUAGAAAUAGCAAGU sg UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGA GUCGGUGCUUUU CRxxxxxx sgRNA mN*mN*mN*NNNNNNNNNNNNNNNNNGUUUUAGAGCUAGAAAUA OMePS sg GCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGG or CACCGAGUCGGUGCmU*mU*mU*U CRxxxxxx sg OMePS CRxxxxxx sgRNA N*N*N*NNNNNNNNNNNNNNNNNGUUUUAGAGCUAGAAAUAGCAA PS sg or GUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACC CRxxxxxx GAGUCGGUGCU*U*U*U sg PS CRxxxxxx dgRNA NNNNNNNNNNNNNNNNNNNNGUUUUAGAGCUAUGCUGUUUUG and AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUG AAAAAGUGGCACCGAGUCGGUGCUUUUUUU (SEQ ID NO: 6660) CRxxxxxx dgRNA mN*mN*mN*NNNNNNNNNNNNNNNNNGUUUUAGAGCUAUGCUGU OMePS U*mU*mU*mG and AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUG AAAAAGUGGCACCGAGUCGGUGCUUUUUUU (SEQ ID NO: 6660) CRxxxxxx dgRNA N*N*N*NNNNNNNNNNNNNNNNNGUUUUAGAGCUAUGCUGUU*U* PS U*G and AACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUG AAAAAGUGGCACCGAGUCGGUGCUUUUUUU (SEQ ID NO: 6660)

TABLE 37 Top indels observed for each gRNA (targeting domain and format) from NGS sequencing at Day 6 post-RNP introduction. gRNA sequences are as indicated in Table 36. Capital letters are the naturally occurring nucleotides at and near the target sequence. Deletions relative to the unmodified target sequence are shown as “-”; insertions are shown as lowercase letters. gRNA targeting % of domain ID all Indel and format Variant Read (Genomic Sequence) reads length g8 dgRNA ACATTCTTATTTTTATCGAGCACAAACGGAAACAATG----- 47.57% −5 OMePS GCAGCCTCTGCTTAGAAAAAGCTGTGGATAAGCCACCT g8 dgRNA ACATTCTTATTTTTATCGAGCACAAACGGAAACAATG- 13.92% −1 OMePS AATGGCAGCCTCTGCTTAGAAAAAGCTGTGGATAAGCCA CCT g8 dgRNA ACATTCTTATTTTTATCGAGCACAAACGGAAACAATG-- 2.89% −2 OMePS ATGGCAGCCTCTGCTTAGAAAAAGCTGTGGATAAGCCAC CT g8 dgRNA ACATTCTTATTTTTATCGAGCACAAACGGAAACAATGCA-- 2.01% −6 OMePS ----GCCTCTGCTTAGAAAAAGCTGTGGATAAGCCACCT g8 dgRNA ACATTCTTATTTTTATCGAGCACAAACGGAAACAAT- 1.65% −1 OMePS CAATGGCAGCCTCTGCTTAGAAAAAGCTGTGGATAAGCC ACCT g8 dgRNA ACATTCTTATTTTTATCGAGCACAAACGGAAACAAaTGCA 1.53% 1 OMePS ATGGCAGCCTCTGCTTAGAAAAAGCTGTGGATAAGCCAC CT CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCC---- 14.45% −13 ---------CCACCGCATCTCTTTCAGCAGTTGTTTC CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC 7.55% 0 TgCATATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC 7.49% −1 TA-ATATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC 4.94% −13 -------------ACCGCATCTCTTTCAGCAGTTGTTTC CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC 4.33% −4 TA----TCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC 2.83% −2 TA--TATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCC---- 19.29% −13 OMePS sg ---------CCACCGCATCTCTTTCAGCAGTTGTTTC CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC 7.11% 0 OMePS sg TgCATATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC 6.26% −13 OMePS sg -------------ACCGCATCTCTTTCAGCAGTTGTTTC CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC 6.19% −1 OMePS sg TA-ATATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC 5.44% −4 OMePS sg TA----TCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC 2.89% −2 OMePS sg TA--TATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCC---- 15.91% −13 OMePS ---------CCACCGCATCTCTTTCAGCAGTTGTTTC CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC 8.91% 0 OMePS TgCATATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC 4.80% −4 OMePS TA----TCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC 4.59% −13 OMePS -------------ACCGCATCTCTTTCAGCAGTTGTTTC CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC 2.92% −1 OMePS TA-ATATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCtTGTTCTCCTC 1.75% 0 OMePS TACATATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCC---- 13.02% −13 PS ---------CCACCGCATCTCTTTCAGCAGTTGTTTC CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC 8.11% 0 PS TgCATATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC 6.08% −1 PS TA-ATATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC 4.43% −13 PS -------------ACCGCATCTCTTTCAGCAGTTGTTTC CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC 3.86% −4 PS TA----TCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC 2.96% −2 PS TA--TATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCC---- 17.48% −13 PS sg ---------CCACCGCATCTCTTTCAGCAGTTGTTTC CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC 7.01% −13 PS sg -------------ACCGCATCTCTTTCAGCAGTTGTTTC CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC 6.84% 0 PS sg TgCATATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC 6.05% −4 PS sg TA----TCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC 4.59% −2 PS sg TA--TATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC 3.53% −1 PS sg TA-ATATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCC---- 10.58% −13 sg ---------CCACCGCATCTCTTTCAGCAGTTGTTTC CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC 9.11% 0 sg TgCATATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC 6.47% −1 sg TA-ATATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC 4.78% −2 sg TA--TATCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC 4.06% −13 sg -------------ACCGCATCTCTTTCAGCAGTTGTTTC CR001028 TTCTGTCATGTGTGTCTTGACTCAGAAACCCTGTTCTCCTC 3.41% −4 sg TA----TCTCCCCACCGCATCTCTTTCAGCAGTTGTTTC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTC-------- 8.30% −13 ------TTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTgCATATCTCCCCA 4.39% 0 CCGCATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC 2.61% −5 A-----TCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC 2.18% −1 ACC-CATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCtTGTTCTCCTCTACATATCTCCCCA 2.12% 0 CCGCATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC 2.10% −2 ACC--ATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTC-------- 10.40% −13 IDT -----TTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC 4.56% 1 IDT ACCGgCATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC 3.83% −1 IDT AC-GCATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC 3.68% −2 IDT ACC--ATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC 2.87% −5 IDT A-----TCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCT---------- 2.54% −15 IDT -----TTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTC-------- 9.90% −13 -----TTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC 4.63% 1 ACCGgCATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC 3.71% −1 ACC-CATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC 2.39% −2 ACC--ATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTgCATATCTCCCCA 2.03% 0 CCGCATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC 1.95% −5 A-----TCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTC-------- 19.91% −13 OMePS sg -----TTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC 5.76% −1 OMePS sg ACC-CATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC 3.09% 1 OMePS sg ACCGgCATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC 3.03% −4 OMePS sg ACCG----TCTTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC 2.98% −6 OMePS sg AC------TCTTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTgCATATCT---------- 2.81% −15 OMePS sg -----TTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTC-------- 8.52% −13 OMePS -----TTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTgCATATCTCCCCA 5.21% 0 OMePS CCGCATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC 2.63% 1 OMePS ACCGgCATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC 2.25% −1 OMePS AC-GCATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC 1.81% −5 OMePS A-----TCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC 1.77% −1 OMePS ACC-CATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTC-------- 5.99% −13 PS -----TTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTgCATATCTCCCCA 4.09% 0 PS CCGCATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC 3.90% 1 PS ACCGgCATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC 3.59% −5 PS A-----TCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC 2.86% −1 PS ACC-CATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC 2.39% −2 PS ACC--ATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTC-------- 11.86% −13 PS sg -----TTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC 5.20% −1 PS sg ACC-CATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC 3.65% 1 PS sg ACCGgCATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC 3.33% −2 PS sg ACC--ATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC 2.92% −5 PS sg A-----TCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACAT--------------- 2.14% −15 PS sg CTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTC-------------------------- 2.08% −26 PS sg TTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTC-------- 11.22% −13 sg -----TTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC 4.64% −1 sg ACC-CATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC 2.78% 1 sg ACCGgCATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC 2.73% −5 sg A-----TCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC 2.34% −1 sg AC-GCATCTCTTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001030 TCTTGACTCAGAAACCCTGTTCTCCTCTACATATCTCCCC 2.29% −6 sg AC------TCTTTCAGCAGTTGTTTCTAAAAATATCCTCC CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC 4.26% 1 GGTAGgCCACTTAAATGCTTACCAACAGTAGAATTGATAA AT CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC- 3.80% −7 ------ACTTAAATGCTTACCAACAGTAGAATTGATAAAT CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC 1.32% 1 GGTAaGCCACTTAAATGCTTACCAACAGTAGAATTGATAA AT CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC 0.98% −8 GGTA--------AATGCTTACCAACAGTAGAATTGATAAAT CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC 0.97% −7 GGT-------TAAATGCTTACCAACAGTAGAATTGATAAAT CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAA----- 0.85% −6 -GCCACTTAAATGCTTACCAACAGTAGAATTGATAAAT CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC 0.73% −1 GGT- GCCACTTAAATGCTTACCAACAGTAGAATTGATAAAT CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC 19.40% 1 OMePS sg GGTAGgCCACTTAAATGCTTACCAACAGTAGAATTGATAA AT CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC- 7.73% −7 OMePS sg ------ACTTAAATGCTTACCAACAGTAGAATTGATAAAT CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAA------- 2.97% −7 OMePS sg GCCACTTAAATGCTTACCAACAGTAGAATTGATAAAT CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC 2.78% −8 OMePS sg GGTA--------AATGCTTACCAACAGTAGAATTGATAAAT CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC 2.27% 1 OMePS sg GGTAaGCCACTTAAATGCTTACCAACAGTAGAATTGATAA AT CR001137 AAATGCTTATGACAGCAATAAT----------------------------------- 2.06% −35 OMePS sg TACCAACAGTAGAATTGATAAAT CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAA----- 2.04% −16 OMePS sg -----------TGCTTACCAACAGTAGAATTGATAAAT CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC 5.27% 1 OMePS GGTAGgCCACTTAAATGCTTACCAACAGTAGAATTGATAA AT CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC- 4.66% −7 OMePS ------ACTTAAATGCTTACCAACAGTAGAATTGATAAAT CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC 2.38% −8 OMePS GGTA--------AATGCTTACCAACAGTAGAATTGATAAAT CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC 1.91% −7 OMePS GGT-------TAAATGCTTACCAACAGTAGAATTGATAAAT CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC 1.72% 1 OMePS GGTAaGCCACTTAAATGCTTACCAACAGTAGAATTGATAA AT CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAA------- 1.03% −7 OMePS GCCACTTAAATGCTTACCAACAGTAGAATTGATAAAT CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCA-------- 0.82% −8 OMePS GCCACTTAAATGCTTACCAACAGTAGAATTGATAAAT CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC- 7.49% −7 PS ------ACTTAAATGCTTACCAACAGTAGAATTGATAAAT CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC 6.85% 1 PS GGTAGgCCACTTAAATGCTTACCAACAGTAGAATTGATAA AT CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC 2.64% −8 PS GGTA--------AATGCTTACCAACAGTAGAATTGATAAAT CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC 2.11% 1 PS GGTAaGCCACTTAAATGCTTACCAACAGTAGAATTGATAA AT CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC 1.91% −3 PS GG---CCACTTAAATGCTTACCAACAGTAGAATTGATAAAT CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAAC--- 1.81% −10 PS -------TTAAATGCTTACCAACAGTAGAATTGATAAAT CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC 1.28% −7 PS GGT-------TAAATGCTTACCAACAGTAGAATTGATAAAT CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC 11.90% 1 PS sg GGTAGgCCACTTAAATGCTTACCAACAGTAGAATTGATAA AT CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC- 7.45% −7 PS sg ------ACTTAAATGCTTACCAACAGTAGAATTGATAAAT CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC 4.87% −25 PS sg GGTAG-------------------------AATTGATAAAT CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC 3.82% −1 PS sg GGT- GCCACTTAAATGCTTACCAACAGTAGAATTGATAAAT CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC 3.57% 1 PS sg GGTAaGCCACTTAAATGCTTACCAACAGTAGAATTGATAA AT CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC 2.81% −1 PS sg GGTA- CCACTTAAATGCTTACCAACAGTAGAATTGATAAAT CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC 2.35% −3 PS sg GGTA---ACTTAAATGCTTACCAACAGTAGAATTGATAAAT CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC- 6.84% −7 sg ------ACTTAAATGCTTACCAACAGTAGAATTGATAAAT CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC 4.54% 1 sg GGTAGgCCACTTAAATGCTTACCAACAGTAGAATTGATAA AT CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC 2.46% 1 sg GGTAaGCCACTTAAATGCTTACCAACAGTAGAATTGATAA AT CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC 1.83% −7 sg GGT-------TAAATGCTTACCAACAGTAGAATTGATAAAT CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC 1.11% −8 sg GGTA--------AATGCTTACCAACAGTAGAATTGATAAAT CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC 0.78% −4 sg GGTA----CTTAAATGCTTACCAACAGTAGAATTGATAAAT CR001137 AAATGCTTATGACAGCAATAATCATAAAAACCTCAAACC 0.72% 1 sg GGTAtGCCACTTAAATGCTTACCAACAGTAGAATTGATAA AT CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCTG---- 29.13% −4 GGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCT- 4.65% −1 ACTGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAA TTGA CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGGAC----- 4.27% −5 TGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATT GA CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGG---------- 1.47% −10 GCAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGGAC---------- 1.14% −10 AGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA CR001221 TAGCATCTACTCTTGTTCAGG------------------------- 1.04% −25 TAAGAGTGGTGATTAATAGATAGGGACAAATTGA CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCTtACT 0.86% 0 GGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCTG---- 26.33% −4 OMePS sg GGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCT- 15.83% −1 OMePS sg ACTGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAA TTGA CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGGAC----- 6.26% −5 OMePS sg TGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATT GA CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCTG-- 3.75% −2 OMePS sg TGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATT GA CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCTGtAC 2.61% 1 OMePS sg TGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATT GA CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGGAC---------- 2.15% −10 OMePS sg AGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCTGAaC 1.82% 1 OMePS sg TGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATT GA CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCTG---- 32.73% −4 OMePS GGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCT- 6.46% −1 OMePS ACTGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAA TTGA CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGGAC----- 5.49% −5 OMePS TGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATT GA CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGG----------- 3.16% −11 OMePS CAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGG---------- 2.03% −10 OMePS GCAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCTGtAC 1.53% 1 OMePS TGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATT GA CR001221 TAGCATCTACTCTTGTTCAGGAAACAATG------------ 1.05% −12 OMePS GGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCTG---- 33.94% −4 PS GGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCT- 7.39% −1 PS ACTGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAA TTGA CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGGAC----- 5.05% −5 PS TGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATT GA CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGGAC---------- 4.03% −10 PS AGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCTGtAC 1.52% 1 PS TGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATT GA CR001221 TAGCATCTACTCTTGTTCAGGAAACAATG------------ 1.48% −12 PS GGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGG----------- 1.43% −11 PS CAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCTG---- 27.00% −4 PS sg GGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCT- 13.43% −1 PS sg ACTGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAA TTGA CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGGAC----- 6.57% −5 PS sg TGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATT GA CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCTGtAC 4.28% 1 PS sg TGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATT GA CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGGACC-- 3.13% −2 PS sg ACTGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAA TTGA CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGGAC---------- 2.40% −10 PS sg AGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCTG------ 2.13% −8 PS sg --GTAAGAGTGGTGATTAATAGATAGGGACAAATTGA CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCTG---- 26.35% −4 sg GGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCT- 8.55% −1 sg ACTGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAA TTGA CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGGAC----- 7.25% −5 sg TGGGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATT GA CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGGAC---------- 2.41% −10 sg AGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGG----------- 1.90% −11 sg CAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA CR001221 TAGCATCTACTCTTGTTCAGGAAACAATGAGGACCTG------ 1.82% −9 sg ---TAAGAGTGGTGATTAATAGATAGGGACAAATTGA CR001221 TAGCATCTACTCTTGTTCAGGAAACAATG------------ 1.81% −12 sg GGCAGTAAGAGTGGTGATTAATAGATAGGGACAAATTGA CR003035 CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC 12.23% −3 CATG---AGTCTGAGGTGCCTATAGGACATCTATATAAATA CR003035 CTGGAAGAGAAAtAGTTTTAGTATAACAAGTGAAATACCC 8.25% 0 ATGCTGAGTCTGAGGTGCCTATAGGACATCTATATAAATA CR003035 CTGGAAGAGAAAtAGTTTTAGTATAACAAGTGAAATACCC 4.47% −3 ATG---AGTCTGAGGTGCCTATAGGACATCTATATAAATA CR003035 CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC 3.60% −1 CAT- CTGAGTCTGAGGTGCCTATAGGACATCTATATAAATA CR003035 CTGGAAGAGAAACAGTTTTAGTATAACAAGTGA------------- 2.79% −14 -GTCTGAGGTGCCTATAGGACATCTATATAAATA CR003035 CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC 2.55% −2 CATG-- GAGTCTGAGGTGCCTATAGGACATCTATATAAATA CR003035 CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATAC--- 1.68% −6 ---TGAGTCTGAGGTGCCTATAGGACATCTATATAAATA CR003035 CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC 13.59% −3 OMePS sg CATG---AGTCTGAGGTGCCTATAGGACATCTATATAAATA CR003035 CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC 5.56% −2 OMePS sg CA--CTGAGTCTGAGGTGCCTATAGGACATCTATATAAATA CR003035 CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC 5.34% −1 OMePS sg CAT- CTGAGTCTGAGGTGCCTATAGGACATCTATATAAATA CR003035 CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC 5.30% −2 OMePS sg CATG-- GAGTCTGAGGTGCCTATAGGACATCTATATAAATA CR003035 CTGGAAGAGAAACAGTTTTAGTATAACAAGTGA------------- 4.70% −14 OMePS sg -GTCTGAGGTGCCTATAGGACATCTATATAAATA CR003035 CTGGAAGAGAAAtAGTTTTAGTATAACAAGTGAAATACCC 4.44% −3 OMePS sg ATG---AGTCTGAGGTGCCTATAGGACATCTATATAAATA CR003035 CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC 2.05% −1 OMePS sg CATG- TGAGTCTGAGGTGCCTATAGGACATCTATATAAATA CR003035 CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC 9.22% −3 OMePS CATG---AGTCTGAGGTGCCTATAGGACATCTATATAAATA CR003035 CTGGAAGAGAAAtAGTTTTAGTATAACAAGTGAAATACCC 7.81% 0 OMePS ATGCTGAGTCTGAGGTGCCTATAGGACATCTATATAAATA CR003035 CTGGAAGAGAAAtAGTTTTAGTATAACAAGTGAAATACCC 3.79% −3 OMePS ATG---AGTCTGAGGTGCCTATAGGACATCTATATAAATA CR003035 CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC 2.63% −1 OMePS CAT- CTGAGTCTGAGGTGCCTATAGGACATCTATATAAATA CR003035 CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC 2.00% −2 OMePS CA--CTGAGTCTGAGGTGCCTATAGGACATCTATATAAATA CR003035 CTGGAAGAGAAACAGTTTTAGTATAACAAGTGA------------- 1.92% −14 OMePS -GTCTGAGGTGCCTATAGGACATCTATATAAATA CR003035 CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC- 1.69% −5 OMePS ----TGAGTCTGAGGTGCCTATAGGACATCTATATAAATA CR003035 CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC 13.91% −3 PS CATG---AGTCTGAGGTGCCTATAGGACATCTATATAAATA CR003035 CTGGAAGAGAAAtAGTTTTAGTATAACAAGTGAAATACCC 6.11% −3 PS ATG---AGTCTGAGGTGCCTATAGGACATCTATATAAATA CR003035 CTGGAAGAGAAAtAGTTTTAGTATAACAAGTGAAATACCC 3.77% 0 PS ATGCTGAGTCTGAGGTGCCTATAGGACATCTATATAAATA CR003035 CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC 3.64% −1 PS CAT- CTGAGTCTGAGGTGCCTATAGGACATCTATATAAATA CR003035 CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC 2.39% −2 PS CATG-- GAGTCTGAGGTGCCTATAGGACATCTATATAAATA CR003035 CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC 2.16% −2 PS CA--CTGAGTCTGAGGTGCCTATAGGACATCTATATAAATA CR003035 CTGGAAGAGAAAtAGTTTTAGTATAACAAGTGAAATACCC 1.87% −1 PS AT-CTGAGTCTGAGGTGCCTATAGGACATCTATATAAATA CR003035 CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC 8.32% −1 PS sg CAT- CTGAGTCTGAGGTGCCTATAGGACATCTATATAAATA CR003035 CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC 6.41% −3 PS sg CATG---AGTCTGAGGTGCCTATAGGACATCTATATAAATA CR003035 CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC 4.19% −2 PS sg CATG-- GAGTCTGAGGTGCCTATAGGACATCTATATAAATA CR003035 CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC 4.08% −2 PS sg CA--CTGAGTCTGAGGTGCCTATAGGACATCTATATAAATA CR003035 CTGGAAGAGAAAtAGTTTTAGTATAACAAGTGAAATACCC 3.31% −1 PS sg AT-CTGAGTCTGAGGTGCCTATAGGACATCTATATAAATA CR003035 CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC 2.99% −4 PS sg C----TGAGTCTGAGGTGCCTATAGGACATCTATATAAATA CR003035 CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC- 2.23% −5 PS sg ----TGAGTCTGAGGTGCCTATAGGACATCTATATAAATA CR003035 CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC 10.92% −3 sg CATG---AGTCTGAGGTGCCTATAGGACATCTATATAAATA CR003035 CTGGAAGAGAAAtAGTTTTAGTATAACAAGTGAAATACCC 6.05% −3 sg ATG---AGTCTGAGGTGCCTATAGGACATCTATATAAATA CR003035 CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC 5.42% −1 sg CAT- CTGAGTCTGAGGTGCCTATAGGACATCTATATAAATA CR003035 CTGGAAGAGAAAtAGTTTTAGTATAACAAGTGAAATACCC 4.55% 0 sg ATGCTGAGTCTGAGGTGCCTATAGGACATCTATATAAATA CR003035 CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC 4.53% −2 sg CA--CTGAGTCTGAGGTGCCTATAGGACATCTATATAAATA CR003035 CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC 3.59% −2 sg CATG-- GAGTCTGAGGTGCCTATAGGACATCTATATAAATA CR003035 CTGGAAGAGAAACAGTTTTAGTATAACAAGTGAAATACC 2.30% −4 sg C----TGAGTCTGAGGTGCCTATAGGACATCTATATAAATA CR001128 GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA 10.38% −1 GGA-GGGTTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGG CR001128 GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA 5.87% −4 GG----GTTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGG CR001128 GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA 5.50% 1 GGAAaGGGTTTGGCCTCTGATTAGGGTGGGGGCGTGGGT GG CR001128 GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA 4.87% −5 GG-----TTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGG CR001128 GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGC-------- 4.61% −36 ----------------------------GTGGGTGG CR001128 GTCTAGTGCAAGCTAACAaC---------------------------- 2.38% −28 ATCACAGGCTCCAGGATAGGGGGCGTGGGTGG CR001128 GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA 2.00% −2 GGA--GGTTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGG CR001128 GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA 7.56% −23 OMePS GG-----------------------TGGGGGCGTGGGTGG CR001128 GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA 6.53% −4 OMePS GG----GTTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGG CR001128 GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA 6.18% −5 OMePS GG-----TTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGG CR001128 GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA 6.06% −1 OMePS GGA-GGGTTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGG CR001128 GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA 3.92% 1 OMePS GGAAaGGGTTTGGCCTCTGATTAGGGTGGGGGCGTGGGT GG CR001128 GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA 2.55% −10 OMePS GG----------CCTCTGATTAGGGTGGGGGCGTGGGTGG CR001128 GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA 10.12% −1 sg GGA-GGGTTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGG CR001128 GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA 7.05% −5 sg GG-----TTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGG CR001128 GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA 4.59% −4 sg GG----GTTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGG CR001128 GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA 4.24% 1 sg GGAAaGGGTTTGGCCTCTGATTAGGGTGGGGGCGTGGGT GG CR001128 GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA 2.21% −27 sg GG---------------------------GGCGTGGGTGG CR001128 GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA 1.66% −30 sg G------------------------------CGTGGGTGG CR001128 GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGC-------- 1.48% −17 sg ---------CTCTGATTAGGGTGGGGGCGTGGGTGG CR001128 GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA 10.59% −5 sg OMePS GG-----TTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGG CR001128 GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA 7.59% −4 sg OMePS GG----GTTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGG CR001128 GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA 5.92% −1 sg OMePS GGA-GGGTTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGG CR001128 GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA 3.38% 1 sg OMePS GGAAaGGGTTTGGCCTCTGATTAGGGTGGGGGCGTGGGT GG CR001128 GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA 2.49% 2 sg OMePS GGAAGagGGTTTGGCCTCTGATTAGGGTGGGGGCGTGGGT GG CR001128 GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA 1.95% −16 sg OMePS GGA----------------TTAGGGTGGGGGCGTGGGTGG CR001128 GTCTAGTGCAAGCTAACAGTTGCTTTTATCACAGGCTCCA 1.85% −2 sg OMePS GGA--GGTTTGGCCTCTGATTAGGGTGGGGGCGTGGGTGG CR000312 TATCACAGGCTCCAGGAAGGGTTTGGCCTCTGATTAGG- 11.83% −1 TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTC TC CR000312 TATCACAGGCTCCAGGAAGGGTTTGG---------------- 5.11% −16 GGGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTCTC CR000312 TATCACAGGCTCCAGGAAGGGTTTGGC------------------- 4.33% −19 GTGGGTGGGGTAGAAGAGGACTGGCAGACCTCTC CR000312 TATCACAGGCTCCAGGAAGGGTTTGGCCTCTGATT-- 3.63% −2 GGTGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCAGAC CTCTC CR000312 TATCACAGGCTCCAGGAAGGG----------------------- 2.50% −23 GCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTCTC CR000312 TATCACAGGCTCCAGGAAGGGTTTGGCCTCTG------ 2.47% −6 GTGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCT CTC CR000312 TATCACAGGCTCCAGGAAGGGTTTGGCCTCTG--------- 2.35% −9 GGGGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTCTC CR000312 TATCACAGGCTCCAGGAAGGGTTTGGCCTCTGATTAGG- 12.06% −1 OMePS TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTC TC CR000312 TATCACAGGCTCCAGGAAGGGTTTGG------------- 4.75% −13 OMePS TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTC TC CR000312 TATCACAGGCTCCAGGAAGGGTTTGGCCTCTGATT-- 4.32% −2 OMePS GGTGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCAGAC CTCTC CR000312 TATCACAGGCTCCAGGAAGGGTTTGGC------------------- 3.97% −19 OMePS GTGGGTGGGGTAGAAGAGGACTGGCAGACCTCTC CR000312 TATCACAGGCTCCAGGAAGGGTTTGG---------------- 3.28% −16 OMePS GGGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTCTC CR000312 TATCACAGGCTCCAGGAAGGGTTTGGCCTCTGATTAGaGG 3.25% 1 OMePS TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTC TC CR000312 TATCACAGGCTCCAGGAAGGGTTTGGCCTCTGATTAG-- 1.91% −2 OMePS TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTC TC CR000312 TATCACAGGCTCCAGGAAGGGTTTGGCCTCTGATTAG-- 6.69% −2 sg TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTC TC CR000312 TATCACAGGCTCCAGGAAGGGTTTGGCCTCTGATTAGG- 6.28% −1 sg TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTC TC CR000312 TATCACAGGCTCCAGGAAGGGTTTGGCCTCTGA-------------- 4.58% −29 sg ---------------AGGACTGGCAGACCTCTC CR000312 TATCACAGGCTCCAGGAAGGGTTTGGCCTCTGATTAGaGG 3.83% 1 sg TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTC TC CR000312 TATCACAGGCTCCAGGAAGGGTTTGG---------------- 3.74% −16 sg GGGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTCTC CR000312 TATCACAGGCTCCAGGAAGGGTTTGGCCTCTG--------- 3.66% −9 sg GGGGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTCTC CR000312 TATCACAGGCTCCAGGAAGGGTTTGGCCTCTGATTAGGG- 3.19% −6 sg -----CGTGGGTGGGGTAGAAGAGGACTGGCAGACCTCTC CR000312 TATCACAGGCTCCAGGAAGGGTTTGG------------- 3.18% −13 sg TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTC TC CR000312 TATCACAGGCTCCAGGAAGGGTTTGGCCTCTGATTAGG- 12.59% −1 sg OMePS TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTC TC CR000312 TATCACAGGCTCCAGGAAGGGTTTGGCCTCTGATT-- 7.73% −2 sg OMePS GGTGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCAGAC CTCTC CR000312 TATCACAGGCTCCAGGAAGGGTTTGGCCTCTG--------- 6.49% −9 sg OMePS GGGGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTCTC CR000312 TATCACAGGCTCCAGGAAGGGTTTGG---------------- 5.32% −16 sg OMePS GGGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTCTC CR000312 TATCACAGGCTCCAGGAAGGGTTTGGC------------------- 3.89% −19 sg OMePS GTGGGTGGGGTAGAAGAGGACTGGCAGACCTCTC CR000312 TATCACAGGCTCCAGGAAGGG---------------------- 2.50% −22 sg OMePS GGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTCTC CR000312 TATCACAGGCTCCAGGAAGGGTTTGG------------- 2.50% −13 sg OMePS TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTC TC CR000312 TATCACAGGCTCCAGGAAGGGTTTGGCCTCTGATTAG-- 2.25% −2 sg OMePS TGGGGGCGTGGGTGGGGTAGAAGAGGACTGGCAGACCTC TC CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGG---------- 12.51% −10 ACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTAT- 8.89% −1 CTAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTT CTA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTATAaC 7.30% 1 TAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTC TA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGA------------- 6.20% −13 CTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA CR003085 ATGTAAGGAGGATGAGCCACATGGTA-------------- 3.50% −14 AGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTA----- 3.09% −5 AGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTATA--- 2.29% −3 AGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTATA- 1.64% −1 TAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTC TA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGG--------- 1.43% −9 TAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTC TA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTATA-- 1.39% −2 AAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTATAaC 13.65% 1 OMePS sg TAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTC TA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGG---------- 10.96% −10 OMePS sg ACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGA------------- 8.21% −13 OMePS sg CTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTAT- 8.15% −1 OMePS sg CTAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTT CTA CR003085 ATGTAAGGAGGATGAGCCACATGGTA-------------- 6.29% −14 OMePS sg AGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTA----- 4.53% −5 OMePS sg AGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTATA--- 3.60% −3 OMePS sg AGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTA-- 3.47% −2 OMePS sg CTAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTT CTA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTATA- 1.30% −1 OMePS sg TAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTC TA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGG------------------- 1.00% −37 OMePS sg ------------------TTATATCCTTCTA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTATAaC 10.09% 1 OMePS TAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTC TA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGG---------- 9.05% −10 OMePS ACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTAT- 6.52% −1 OMePS CTAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTT CTA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGA------------- 4.94% −13 OMePS CTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA CR003085 ATGTAAGGAGGATGAGCCACATGGTA-------------- 4.55% −14 OMePS AGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTA----- 2.40% −5 OMePS AGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTA-- 2.00% −2 OMePS CTAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTT CTA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTATA--- 1.82% −3 OMePS AGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTATA- 1.57% −1 OMePS TAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTC TA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGGT---------- 1.16% −34 OMePS ------------------------TATATCCTTCTA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGG---------- 15.06% −10 PS ACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTAT- 11.15% −1 PS CTAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTT CTA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTATAaC 8.37% 1 PS TAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTC TA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGA------------- 7.44% −13 PS CTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA CR003085 ATGTAAGGAGGATGAGCCACATGGTA-------------- 5.33% −14 PS AGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTA----- 3.58% −5 PS AGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTATA--- 3.50% −3 PS AGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTA-- 2.05% −2 PS CTAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTT CTA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGG-------------- 1.39% −14 PS ACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTATA- 0.86% −1 PS TAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTC TA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTAT- 12.62% −1 PS sg CTAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTT CTA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTATAaC 11.73% 1 PS sg TAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTC TA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGG---------- 8.86% −10 PS sg ACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGA------------- 6.59% −13 PS sg CTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA CR003085 ATGTAAGGAGGATGAGCCACATGGTA------------- 4.88% −14 PS sg AGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTATA--- 3.68% −3 PS sg AGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTA-- 3.62% −2 PS sg CTAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTT CTA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTATA- 3.48% −1 PS sg TAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTC TA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTA----- 2.90% −5 PS sg AGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA CR003085 ATGTAAGGAGGATGAGCCACATGGTAT------------ 1.10% −12 PS sg AAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGG---------- 11.79% −10 sg ACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTAT- 9.21% −1 sg CTAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTT CTA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTATAaC 6.84% 1 sg TAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTC TA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGA------------- 6.44% −13 sg CTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA CR003085 ATGTAAGGAGGATGAGCCACATGGTA-------------- 4.12% −14 sg AGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTA----- 3.46% −5 sg AGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTATA--- 3.22% −3 sg AGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTA-- 1.65% −2 sg CTAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTT CTA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGGGAGGTATA- 1.07% −1 sg TAAGGACTCTAGGGTCAGAGAAATATGGGTTATATCCTTC TA CR003085 ATGTAAGGAGGATGAGCCACATGGTATGG-------------- 0.95% −14 sg ACTCTAGGGTCAGAGAAATATGGGTTATATCCTTCTA

The genome edited and unedited HSPC were analyzed for proliferation and HbF upregulation in a three-stage erythroid differentiation cell culture protocol. The genome edited and unedited HSPC were analyzed by flow cytometry for expression levels of fetal globin and at day 7 for two erythroid cell surface markers, transferrin receptor (CD71) and glycophorin A (CD235a) using antibodies conjugated to fluorescent dyes. The live cells were identified and gated by exclusion of Live/Dead Fixable Dead Cell Stain. Genome editing with the included HPFH region targeting and BCL11A erythroid enhancer targeting gRNAs did not adversely affect erythroid differentiation as the cultured cells showed percentages of CD71+ cells consistent with erythroblasts similar to unedited cells at day 7 of differentiation, although Protocol 1 and Protocol 2 differed in percentages of CD71+ across conditions (FIG. 44). Cultures treated with the included HPFH region targeting and BCL11A erythroid enhancer targeting gRNAs resulted in similar patterns of relative changes in the percentage of erythroid cells containing HbF compared to mock electroporated cells throughout the 21 day culture period and between the two protocols (FIG. 45, FIG. 46 and FIG. 47). HbF was induced in cells exposed of RNPs and maintained in either Protocol 1 or Protocol 2, however, the percentage of cells that were HbF positive tended to be lower across conditions and timepoints with Protocol 2 (FIG. 45, FIG. 46 and FIG. 47). Induction of HbF was most pronounced with gRNAs consisting of target domains CR001030, CR00312 and CR001128, particularly at the later timepoints (FIG. 45, FIG. 46 and FIG. 47). Across targeting domains, sgRNAs trended to higher induction of HbF than dgRNAs, particularly OMePS modified sgRNAs (FIG. 45, FIG. 46 and FIG. 47). Relatively low induction of HbF with targeting domain CR001137 may be explained by the lower level of editing at this target site (FIG. 43, FIG. 45-FIG. 47). Induction of HbF positive cells by dgRNA including the targeting domain of g8 targeting exon 2 of BCL11A was also observed in parallel (FIG. 45-FIG. 47). An increase in HbF-containing erythrocytes derived from genome edited cells is likely to have therapeutic implications by reduced sickling. Edited cells were capable of proliferating in erythroid differentiation conditions (9 to 53-fold at day 7 and 36 to 143-fold at day 21, FIG. 48), however, in some cases, proliferation was suppressed relative to unedited control cells (14-83% of unedited control at day 7 and 18-95% of unedited control at day 21) (FIG. 48). Lowest proliferation was observed with the cells edited by dgRNA including the targeting domain of g8 targeting exon 2 of BCL11A (30% of unedited control at day 7 and 18% of unedited control at day 21) and with many of the OMePS modified sgRNAs (FIG. 48).

Example 5 Excision Using Two gRNAs to the HPFH Region

Primary human CD34+ HSPCs were electroporated with RNP containing two different gRNA molecules to different sites within the HPFH region. For each RNP, dgRNA molecules as described above, were used. Briefly, RNP comprising a dgRNA targeting a first site within the French HPFH region and RNP comprising a dgRNA targeting a second site within the French HPFH region were combined, and electroporated into CD34+ HSPCs in the following ratios: 0.5× first dgRNA RNP+0.5× second dgRNA RNP; 1.0×g2 dgRNA (“g2”=positive control comprising a targeting domain of CR000088, which targets a coding sequence of the BCL11a gene); no RNPs (“control”). Cells were cultured as described above, and differentiated into erythrocytes using the protocol described above (see FIG. 17). Fetal hemoglobin expression was assessed. The results are shown in FIG. 27 and Table 25. Without being bound by theory, it is believed that simultaneous introduction of RNPs comprising gRNA molecules to two target sequences will cause the deletion (i.e., excision) of the DNA between the two cut sites (e.g., all or most of the DNA between the two cut sites), including any regulatory or coding sequences contained within that region. These results show that RNPs targeting two separate regions within the HPFH region could be delivered simultaneously to CD34+ HSPCs by electroporation and induce fetal hemoglobin expression in edited cells differentiated into erythrocytes.

TABLE 25 Guide RNA targeting domain ID 1/Guide RNA % HbF+ (F cells), average targeting domain ID 2 of replicates CR001016/CR001021 50.9 CR001021/CR001034 53.4 CR001034/CR001037 56.1 CR001037/CR001045 50.6 CR001045/CR001058 45.2 CR001058/CR001065 42.6 CR001065/CR001075 43.3 CR001075/CR001086 40.4 CR001086/CR001096 39.3 CR001096/CR001107 41.6 CR001107/CR001135 45.6 CR001143/CR001151 40.1 CR001151/CR001159 40.9 CR001159/CR001166 42.0 CR001166/CR001173 44.8 CR001173/CR001179 43.1 CR001179/CR001191 41.9 CR001191/CR001199 42.7 CR001199/CR001212 48.3 CR001212/CR001227 45.6 CR001016/CR001034 53.4 CR001034/CR001045 50.0 CR001045/CR001065 44.2 CR001065/CR001086 39.1 CR001086/CR001107 43.4 CR001107/CR001143 44.8 CR001143/CR001159 45.0 CR001159/CR001173 46.6 CR001173/CR001191 44.8 CR001191/CR001212 51.7 CR001021/CR001037 56.9 CR001037/CR001058 48.0 CR001058/CR001075 41.7 CR001075/CR001096 41.5 CR001096/CR001135 44.3 CR001135/CR001151 42.9 CR001151/CR001166 41.9 CR001166/CR001179 40.4 CR001179/CR001199 38.5 CR001199/CR001227 40.0 g2 54.0 ctrl 34.5

Example 6. Potential Off-Target Editing Assessment of gRNAs Targeting the BCL11a Enhancer

An oligo insertion based assay (See, e.g., Tsai et al., Nature Biotechnology. 33, 187-197; 2015) was used to determine potential off-target genomic sites cleaved by Cas9 targeting the BCL11a enhancer.

A total of 28 guides (dual guide RNAs comprising the indicated targeting domain) targeting the BCL11a enhancer and 10 gRNAs targeting the HPFH region were screened in the Cas9-expressing HEK293 cells described above, and the results are plotted in FIG. 33 (BCL11a enhancer) and FIG. 49 (HPFH). With respect to the gRNAs targeting the BCL11a enhancer, the assay identified potential off-target sites for some guides, however targeted deep sequencing was used to determine whether the potential sites were bona fide off-target sites cleaved by Cas9. Using primers that flanked the potential off-target sites, isolated genomic DNA was amplified and the amplicons were sequenced. If the potential off-target site was cleaved by Cas9, indels should be detected at the site. From these follow-on interrogations of the potential off-target sites, no indels were detected at the potential off-target sites for at least three of the guide RNAs: CR000311, CR000312, CR001128. With respect to the gRNAs targeting the BCL11a enhancer, the assay did not identify any potential off-target sites for at least gRNAs CR001137, CR001212, and CR001221. Targeted deep sequencing will be performed to determine whether the potential off target sites identified for the other gRNA molecules are bona-fide off target sites cleaved by Cas9.

Example 7: Evaluation of Cas9 Variants Evaluation in CD34+ Hematopoietic Stem Cells

We evaluated 14 purified Streptococcus pyogenes Cas9 (SPyCas9) proteins by measuring their efficiency of knocking out the beta-2-microglobulin (B2M) gene in primary human hematopoietic stem cells (HSCs). These proteins were divided into 3 groups: the first group consisted of SPyCas9 variants with improved selectivity (Slaymaker et al. 2015, Science 351: 84 (e1.0, e1.1 and K855A); Kleinstiver et al. 2016, Nature 529: 490 (HF)). The second group consisted of wild type SPyCas9 with different numbers and/or positions of the SV40 nuclear localization signal (NLS) and the 6×Histidine (His6) or 8×Histidine (His8) tag with or without a cleavable 1EV site, and a SPyCas9 protein with two cysteine substitutions (C80L, C574E), which have been reported to stabilize Cas9 for structural studies (Nishimasu et al. 2014, Cell 156:935). The third group consisted of the same recombinant SPyCas9 produced by different processes (FIG. 60). B2M knockout was determined by FACS and next generation sequencing (NGS).

Methods Materials

-   1. Neon electroporation instrument (Invitrogen, MPK5000) -   2. Neon electroporation kit (Invitrogen, MPK1025) -   3. crRNA (targeting domain sequence of GGCCACGGAGCGAGACAUCU,     complementary to a sequence in the B2M gene, fused to SEQ ID NO:     6607) -   4. tracrRNA (SEQ ID NO: 6660) -   5. Cas9 storage buffer: 20 mM Tris-Cl, pH 8.0, 200 mM KCl, 10 mM     MgCl₂ -   6. Bone marrow derived CD34+ HSCs (Lonza, 2M-101C) -   7. Cell culture media (Stemcell Technologies, StemSpam SFEM II with     StemSpam CC-100) -   8. FACS wash buffer: 2% FCS in PBS -   9. FACS block buffer: per mL PBS, add 0.5 ug mouse IgG, 150 ug Fc     block, 20 uL FCS -   10. Chelex suspension: 10% Chelex 100 (bioRad, Cat#142-1253) in H₂O -   11. Anti-B2M antibody: Biolegend, cat#316304

Process

Thaw and grow the cells following Lonza's recommendations, add media every 2-3 days. On day 5, pellet the cells at 200×g for 15 min, wash once with PBS, resuspend the cells with T-buffer from NEON kit at 2×10⁴/uL, put on ice. Dilute Cas 9 protein with Cas9 storage buffer to 5 mg/ml. Reconstitute crRNA and tracrRNA to 100 uM with H₂O. The ribonucleoprotein (RNP) complex is made by mixing 0.8 uL each of CAS 9 protein, crRNA and tracrRNA with 0.6 uL of Cas9 storage buffer, incubate at room temperature for 10 min. Mix 7 uL of HSCs with RNP complex for two minutes and transfer the entire 10 uL into a Neon pipette tip, electroporate at 1700v, 20 ms and 1 pulse. After electroporation, immediately transfer cells into a well of 24-well plate containing 1 ml media pre-calibrated at 37° C., 5% CO₂. Harvest cells 72 hrs post-electroporation for FACS and NGS analysis.

FACS: take 250 uL of the cells from each well of 24-well plate, to wells of 96-well U-bottom plate and pellet the cells. Wash once with 2% FCS (fetal calf serum)-PBS. Add 50 uL FACS block buffer to the cells and incubate on ice for 10 minutes, add 1 uL FITC labeled B2M antibody and incubate for 30 minutes. Wash with 150 uL FACS wash buffer once followed by once more with 200 uL FACS wash buffer once. Cells were resuspended in 200 uL FACS buffer FACS analysis.

NGS sample prep: transfer 250 uL of cell suspension from each well of the 24-well plate to a 1.5 ml Eppendorf tube, add 1 mL PBS and pellet the cells. Add 100 uL of Chelex suspension, incubate at 99° C. for 8 minutes and vortex 10 seconds followed by incubating at 99° C. for 8 minutes, vortex 10 seconds. Pellet down the resin by centrifuging at 10,000×g for 3 minutes and the supernatant lysate is used for PCR. Take 4 uL lysate and do PCR reaction with the b2m primers (b2mg67F: CAGACAGCAAACTCACCCAGT, b2mg67R: CTGACGCTTATCGACGCCCT) using Titanium kit (Clonetech, cat#639208) and follow the manufacturer's instruction. The following PCR conditions are used: 5 minutes at 98° C. for 1 cycle; 15 seconds at 95° C., 15 seconds at 62° C., and 1 minute at 72° C. for 30 cycles; and finally 3 minutes at 72° C. for 1 cycle. The PCR product was used for NGS.

Statistics: The percentage of B2M KO cells by FACS and the percentage of indels by NGS are used to evaluate the CAS 9 cleavage efficiency. The experiment was designed with Cas9 as fixed effect. Each experiment is nested within donors, as nested random effects. Therefore, the mixed linear model was applied for the analysis of FACS and NGS data.

Results

In order to normalize the experimental and donor variations, we graphed the relative activity of each protein to iProt105026, the original design with two SV40 NLS flanking the wild type SPyCas9 and the His6 tag at the C-terminal of the protein (FIG. 34). The statistical analysis shows that compared with the reference Cas9 protein iProt105026, iProt106331, iProt106518, iProt106520 and iProt106521 are not significantly different in knocking out B2M in HSCs, while the other variants tested (PID426303, iProt106519, iProt106522, iProt106545, iProt106658, iProt106745, iProt106746, iProt106747, iProt106884) are highly significantly different from the reference iProt105026 in knocking out B2M in HSCs. We found that moving the His6 tag from the C-terminal to N-terminal (iProt106520) did not affect the activity of the protein (FIG. 34). One NLS was sufficient to maintain activity only when it was placed at the C-terminal of the protein (iProt106521 vs. iProt106522, FIG. 34). Proteins purified from process 1 had consistent higher knockout efficiency than those from processes 2 and 3 (iProt106331 vs. iProt106545 & PID426303, FIG. 34). In general, the SPyCas9 variants with a reported improved selectivity were not as active as the wild type SPyCas9 (iProt106745, iProt106746 and iProt106747, FIG. 34). Interestingly iProt106884 did not cut the targeting site. This is consistent with the report by Kleinstiver et al that this variant failed to cut up to 20% of the legitimate targeting sites in mammalian cells (Kleinstiver et al. 2016, Nature 529: 490). Finally, the Cas9 variant with two cysteine substitutions (iProt106518) maintained high levels of enzymatic activity (FIG. 34).

Next, editing efficiency of RNPs comprising different Cas9 variants were tested with either modified or unmodified gRNAs targeting the +58 enhancer region. sgRNA molecules comprising the targeting domains of cr00312 and cr1128 were tested in either unmodified (CR00312=SEQ ID NO: 342; CR001128=SEQ ID NO: 347) or modified (OMePS CR00312=SEQ ID NO: 1762; OMePS CR001128=SEQ ID NO: 1763), and were precomplexed with Cas9 variants shown in Table 35.

TABLE 35 Cas9 variants tested for biological function with +58 enhancer region- targeting gRNA molecules. iProt Code Construct iProt106518 NLS-Cas9(C80L/C574E)-NLS-His6 iProt106331 NLS-Cas9-NLS-His6 iProt106745 NLS-Cas9(K855A)-NLS-His6 iProt106884 NLS-Cas9(HF)-NLS-His6

RNP formed as described above were delivered to HSPC cells as described above, and the cells assessed for % editing (by NGS) and % HbF induction upon erythroid differentiation, as described in these Examples. The results are shown in FIG. 42A (% editing) and FIG. 42B (HbF induction). The results show that varying the Cas9 component between those variants tested did not alter the gene editing efficiency of both unmodified and modified versions of sgRNA CR00312 and CR001128, nor did the Cas9 variants impact the ability of the erythroid-differentiated gene edited cells to produce HbF.

Example 8: Ex Vivo Expansion of Gene Edited HSPCs, and Editing Analysis in HSPC Subsets Expansion of Cells Prior to Gene-Editing

Human bone marrow CD34⁺ cells were purchased from either AllCells (Cat#: ABM017F) or Lonza (Cat#: 2M-101C) and expanded for 2 to 3 days using StemSpan SFEM (StemCell Technologies; Cat no. 09650) supplemented with 50 ng/mL of thrombopoietin (Tpo, Peprotech; Cat#300-18), 50 ng/mL of human Flt3 ligand (Flt-3L, Peprotech; Cat#300-19), 50 ng/mL of human stem cell factor (SCF, Peprotech; Cat#300-07), human interleukin-6 (IL-6, Peprotech; Cat#200-06), 1% L-glutamine; 2% penicillin/streptomycin, and Compound 4 (0.75 μM).

Electroporation of Cas9 and Guide RNA Ribonucleoprotein (RNP) Complexes into Cells

Cas9-guide RNA ribonucleoprotein complexes (RNPs) were prepared immediately prior to electroporation. For formation of RNP using dual guide RNAs, 3 μg of each of crRNA (in 2.24 μL) and tracrRNA (in 1.25 μL) were first denatured at 95° C. for 2 min in separate tubes and then cooled to room temperature. For preparation of Cas9 protein, 7.3 μg of CAS9 protein (in 1.21 μL) was mixed with 0.52 μL of 5×CCE buffer (20 mM HEPES, 100 mM KCL, 5 mM MgCL2, 5% Glycerol and freshly added 1 mM DTT). TracrRNA was first mixed with the Cas9 preparation and incubated at 37° C. for 5 min. The CrRNA was then added to TracrRNA/CAS9 complexes and incubated for 5 min at 37° C. The HSPC were collected by centrifugation at 200×g for 15 min and resuspended in T buffer affiliated with the Neon electroporation kit (Invitrogen; Cat#: MPK1096) at a cell density of 2×10⁷/mL. RNP was mixed with 12 μL of cells by pipetting up and down 3 times gently. To prepare single guide RNA (sgRNA) and Cas9 complexes, 2.25 μg sgRNA (in 1.5 μL) was mixed with 2.25 μg Cas9 protein (in 3 μL) and incubated at RT for 5 min. The sgRNA/Cas9 complex was then mixed with 10.5 μL of 2×10⁷/mL cells by pipetting up and down several times gently and incubated at RT for 2 min. The RNP/cell mixture (10 μL) was transferred into a Neon electroporation probe. Electroporation was performed with Neon transfection system (Invitrogen; MPK5000S) using 1700 volts/20 milliseconds and 1 pulse.

Expansion of Cells after Gene-Editing

After electroporation, the cells were transferred into 0.5 mL pre-warmed StemSpan SFEM medium supplemented with growth factors, cytokines and Compound 4 as described above and cultured at 37° C. for 3 days. After a total of 10 days of cell expansion, 3 days before electroporation and 7 days after electroporation, the total cell number increased 2-7 fold relative to the starting cell number (FIG. 35).

Genomic DNA Preparation

Genomic DNA was prepared from edited and unedited HSPC at 48 hours post-electroporation. Cells were lysed in 10 mM Tris-HCL, pH 8.0; 0.05% SDS and freshly added Protease K of 25 μg/mL and incubated at 37° C. for 1 hour followed by additional incubation at 85° C. for 15 min to inactivate protease K.

T7E1 Assay

To determine editing efficiency of HSPCs, T7E1 assay was performed. PCR was performed using Phusion Hot Start II High-Fidelity kit (Thermo Scientific; Cat#: F-549L) with the following cycling condition: 98° C. for 30″; 35 cycles of 98° C. for 5″, 68° C. for 20′, 72° C. for 30″; 72° C. for 5 min. The following primers were used: forward primer: 5′-AGCTCCAAACTCTCAAACCACAGGG-3′ and reverse primer: 5′-TACAATTTTGGGAGTCCACACGGCA-3′. PCR products were denatured and re-annealed using the following condition: 95° C. for 5 min, 95-85° C. at −2° C./s, 85-25° C. at −0.1° C./s, 4° C. hold. After annealing, 1 μL of mismatch-sensitive T7 E1 nuclease (NEB, Cat# M0302L) was added into 10 μL of PCR product above and further incubated at 37° C. for 15 min for digestion of hetero duplexes, and the resulting DNA fragments were analyzed by agarose gel (2%) electrophoresis. Editing efficiency was quantified using ImageJ software (http://rsb.info.nih.gov/ij/).

PCR Preparation for Next Generation Sequencing (NGS)

To determine editing efficiency more precisely and patterns of insertions and deletions (indels), the PCR products were subjected to next generation sequencing (NGS). The PCR were performed in duplicate using Titanium Taq PCR kit (Clontech Laboratories; Cat#: 639210) with the following cycling condition: 98° C. for 5 min; 30 cycles of 95° C. for 15 seconds, 68° C. for 15 seconds, 72° C. 1 min; 72° C. for 7 min. The following primers were used: forward primer: 5′-AGCTCCAAACTCTCAAACCACAGGG-3′ and reverse primer: 5′-TACAATTTTGGGAGTCCACACGGCA-3′. The PCR products were analyzed by 2% agarose gel electrophoresis and submitted for deep sequencing.

Flow Cytometry Analysis of Editing Efficiency in Hematopoietic Stem and Progenitor Subpopulations.

Cells were subjected to flow cytometry to characterize editing efficiency in stem and progenitor cell (HSPC) subpopulations. The frequencies of HSPC subsets, including CD34+ cells, CD34+CD90+ cells, CD34+CD90+CD45RA− cells, and CD34+CD9O+CD45RA−CD49f+ cells, prior to (48 hours in culture) and after genome editing (10 days in culture; 3 days after genome editing) was determined from sampling aliquots of cell cultures (FIG. 36, FIG. 37, FIG. 38). Cells were incubated with anti-CD34 (BD Biosciences, Cat#555824), anti-CD38 (BD Biosciences, Cat#560677), anti-CD90 (BD Biosciences, Cat#555596), anti-CD45RA (BD Biosciences, Cat#563963), anti-CD49f (BD Biosciences, Cat#562582) in modified FACS buffer, containing PBS supplemented with 0.5% BSA, 2 mM EDTA pH7.4, at 4° C., in dark for 30 min. Cell viability was determined by 7AAD. Cells were washed with modified FACS buffer and multicolor FACS analysis was performed on a Fortessa (BD Biosciences). Flow cytometry results were analyzed using Flowjo software. Genome edited cells grown in the presence of Compound 4 (alone) exhibited detectible levels of all HSPC subsets assessed, including CD34+, CD34+CD90+, CD34+CD9O+CD45RA−, and CD34+CD9O+CD45RA−CD49f+ subsets, indicating that long-term HSC populations persist in cell culture in the presence of Compound 4 (alone) after genome editing (FIG. 38).

Four hours after gene editing, aliquots of cell cultures were sampled and cells were sorted into HSPC subsets (CD34+, CD34+CD38+, CD34+CD38−, CD34+CD38−CD45RA−, CD34+CD38−CD45RA−CD9O+CD49f−, CD34+CD38−CD45RA−CD9O−CD49f−, and CD34+CD38−CD45RA−CD9O−CD49f+ cells) and subjected to NGS to measure the editing efficiency (Table 28). It is important to note that all hematopoietic subsets, including the subsets enriched in long-term HSCs, displayed similarly high gene editing efficiencies (>95%). This high gene editing efficiency in long-term HSCs has significant therapeutic impact as these cells are capable of engrafting patients in the long-term and sustain life-long hematopoietic multi-lineage regeneration.

TABLE 28 Editing efficiency in each HSPC subset measured by NGS. gRNA HSPC subsets Avg (% Indels) Dg CR00312 Total (singlets) 97.98% CD34+CD38−CD45RA− 98.66% CD34+CD38−CD45RA−CD90+CD49f− 98.19% CD34+CD38−CD45RA−CD90−CD49f− 98.70% CD34+CD38−CD45RA−CD90−CD49f+ 98.81% Dg Total (singlets) 97.62% CR001128 CD34+CD38−CD45RA− 95.93% CD34+CD38−CD45RA−CD90−CD49f− 98.00% CD34+CD38−CD45RA−CD90−CD49f+ 99.01%

Example 9 Evaluation of Potential Off-Target Editing HSPC Culture and CRISPR/Cas9 Genome Editing

Methods for RNP generation and cell manipulation are as in Example 4, with the following exceptions. Human CD34⁺ cell culture Human CD34+ cells were either isolated from G-CSF mobilized peripheral blood from adult donors (AllCells, Cat. No. mPB025-Reg.E) using immunoselection (Miltenyi) according to the manufacturer's instructions or derived from bone marrow (Hemacare Corporation, Cat. No. BM34C-3). CD34+ cells were thawed and expanded for 2 days or 5 days prior to RNP delivery. After RNP delivery, cells were either cultured for an additional 13 days in expansion medium or cultured in erythroid differentiation medium for 7 or 11 days as follows. During days 0-7 of culture, EDM was further supplemented with 1 μM hydrocortisone (Sigma H8672), 100 ng/mL human SCF (Life Technologies, Cat. #PHC2113), and 5 ng/mL human IL-3 (Peprotech #10779-598). During days 7-11 of culture, EDM was supplemented with 100 ng/mL of human SCF only. At the conclusion of the culture period, cells were harvested for genomic DNA preparation and analysis.

Assembly of Cas9 and guide RNA ribonucleoprotein (RNP) complexes, preparation of HSPC, and electroporation of RNP into HSPC. The HSPC collected by centrifugation were resuspended in P3 Primary Cell Solution (Lonza cat. No. PBP3-00675). The RNP was mixed with 20 μL of cells by pipetting up and down and incubated at RT for 2 min. The RNP/cell mixture (20 μL) was electroporated using code CM-137 on the 4D-Nucleofector (Lonza). dgRNAs comprising a crRNA having the sequence NNNNNNNNNNNNNNNNNNNNGUUUUAGAGCUAUGCUGUUUUG (where N indicates a residue of the indicated targeting domain) and a tracr having the sequence of SEQ ID NO: 6660 were used.

Genomic DNA Extraction

Genomic DNA was isolated from RNP treated and untreated HSPC using the DNeasy Blood & Tissue Kit (Qiagen, Cat #69506) following the manufacturer's recommendations.

In Silico Identification of Potential gRNA Off-Target Loci

Potential off-target loci for the BCL11A+58 region gRNAs CR00309, CR00311, CR00312, CR00316, CR001125, CR001126, CR001127, and CR001128, and the HPFH region gRNAs CR001028, CR001030, CR001137, CR001221, CR003035, and CR003085 were identified as follows. For each gRNA, the 20 nucleotide gRNA protospacer sequence was aligned to the human genome reference sequence (build GRCh38) using the BFAST sequence aligner (version 0.6.4f, Homer et al, PLoS One, 2009, 4(11), e7767, PMID: 19907642) using standard parameters allowing up to 5 nucleotide mismatches. Loci identified were filtered to only contain sites that are 5′ adjacent to the Cas9 canonical 5′-NGG-3′ PAM sequence (i.e. 5′-off-target locus-PAM-3′). Using the BEDTools script (version 2.11.2, Quinlan and Hall, Bioinformatics, 2010 26(6):841-2, PMID: 20110278) sites with 5 nucleotide mismatches were further filtered against RefSeq gene annotations (Pruitt et al, Nucleic Acids Res., 2014 42(Database issue):D756-63, PMID: 24259432) to only contain loci annotated as exons. Counts of the potential off-target loci identified for the BCL11A+58 region and the HPFH region gRNAs are shown in Tables 1 and 2 respectively.

TABLE 29 Counts of in silico off-target loci identified for the BCL11A +58 region gRNAs CR00309, CR00311, CR00312, CR00316, CR001125, CR001126, CR001127, and CR001128 with 0, 1, 2, 3 and 4 nucleotide mismatches and 5 nucleotide mismatches within RefSeq exons are shown. gRNA targeting Number of off-targets with N mismatches domain ID 0 1 2 3 4 5 RefSeq exons Total sites CR00309 0 0 2 9 77 52 140 CR00311 0 0 3 13 213 38 267 CR00312 0 0 0 6 126 33 165 CR00316 0 0 0 22 234 90 346 CR001125 0 0 1 16 221 83 321 CR001126 0 0 2 26 235 86 349 CR001127 0 0 1 35 331 157 524 CR001128 0 0 0 9 156 42 207

TABLE 30 Counts of in silico off-target loci identified for the HPFH region gRNAs CR001028, CR001030, CR001137, CR001221, CR003035, and CR003085 with 0, 1, 2, 3 and 4 nucleotide mismatches and 5 nucleotide mismatches within RefSeq exons are shown. gRNA targeting Number of off-targets with N mismatches domain ID 0 1 2 3 4 5 RefSeq exons Total sites CR001028 0 0 1 11 154 67 233 CR001030 0 0 0 14 125 85 224 CR001137 0 0 1 6 85 21 113 CR001221 0 0 2 17 166 44 229 CR003035 0 0 4 10 158 77 249 CR003085 0 0 0 5 75 16 96

PCR Primer Design for Targeted Amplification of Potential Off-Target Sites

PCR amplicons targeting potential off-target loci (and the on-target locus) identified for the BCL11A +58 region gRNAs (CR00309, CR00311, CR00312, CR00316, CR001125, CR001126, CR001127, and CR001128) and the HPFH region gRNAs (CR001028, CR001030, CR001137, CR001221, CR003035, and CR003085) were design using Primer3 (version 2.3.6, Untergasser et al, Nucleic Acids Res., 2012 40(15):e115, PMID: 22730293) using default parameters aiming for an amplicon size range of approximately 160-300 base pairs in length with the gRNA protospacer sequence located in the center of the amplicon. For gRNA CR001127 PCR primers were only designed for sites with 0-4 nucleotide mismatches, no primers were designed for sites with 5 nucleotide mismatches within RefSeq exons. Resulting PCR primer pairs and amplicon sequences were checked for uniqueness by BLAST searching (version 2.2.19, Altschul et al, J Mol Biol., 1990, 215(3):403-10, PMID: 2231712) sequences against the human genome reference sequence (build GRCh38). Primer pairs resulting in more than one amplicon sequence were discarded and redesigned. Tables 3 and 5 show counts of successful PCR primer pairs designed for the BCL11A+58 region and the HPFH region gRNAs respectively.

Illumina Sequencing Library Preparation, Quantification and Sequencing

Genomic DNA from RNP treated (2 replicates per gRNA) and untreated (1 replicate per gRNA) HSPC samples was quantified using the Quant-iT PicoGreen dsDNA kit (Thermo Fisher, Cat # P7581) using manufacture's recommendations. Illumina sequencing libraries targeting individual off-target loci (and the on-target locus) were generated for each sample using two sequential PCR reactions. The first PCR amplified the target locus using target specific PCR primers (designed above) that were tailed with universal Illumina sequencing compatible sequences. The second PCR added additional Illumina sequencing compatible sequences to the first PCR amplicon, including sample barcodes to enable multiplexing during sequencing. PCR 1 was performed in a final volume of 10 μL with each reaction containing 3-6 ng of gDNA (equivalent to approximately 500-1000 cells), PCR 1 primer pairs (Integrated DNA Technologies) at a final concentration of 0.25 μM and 1× final concentration of Q5 Hot Start Master Mix (New England BioLabs, Cat #102500-140). PCR 1 left primers were 5′ tailed (i.e. 5′-tail-target specific left primer-3′) with sequence 5′-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG-3′ and right primers were 5′ tailed (i.e. 5′-tail-target specific right primer-3′) with sequence 5′-GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG-3′. PCR 1 was performed on a thermocycler using the following cycling conditions: 1 cycle of 98° C. for 1 min; 25 cycles of 98° C. for 10 sec, 63° C. for 20 sec, and 72° C. for 30 sec; 1 cycle at 72° C. for 2 min. PCR 1 was then diluted 1 in 100 using nuclease free water (Ambion, Cat # AM9932) and used as input into PCR 2. PCR 2 was performed in a final volume of 10 μL with each reaction containing 2 μL of diluted PCR 1 product, PCR 2 primer pairs (Integrated DNA Technologies) at a final concentration of 0.5 μM and 1× final concentration of Q5 Hot Start Master Mix (New England BioLabs, Cat #102500-140). PCR 2 left primer sequence used was 5′-AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTC-3′ and PCR 2 right primer sequence used was 5′-CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTCTCGTGGGCTCGG-3′ where the NNNNNNNN denote an 8 nucleotide barcode sequence used for sample multiplexing as part of the standard Illumina sequencing process. PCR 2 was performed on a thermocycler using the following cycling conditions: 1 cycle of 72° C. for 3 min; 1 cycle of 98° C. for 2 min; 15 cycles of 98° C. for 10 sec, 63° C. for 30 sec, and 72° C. for 2 min. PCR 2 amplicons, now viable Illumina sequencing libraries, were cleaned up using Agencourt AMPure XP beads (Beckman Coulter, Cat # A63882) following the manufacture's recommendations. The cleaned Illumina sequencing libraries were then quantified using standard qPCR quantification methods using Power SYBR Green PCR master mix (Life Technologies, Cat #4367660) and primers specific to the Illumina sequencing library ends (forward primer sequence 5′-CAAGCAGAAGACGGCATACGA-3′ and reverse primer sequence 5′-AATGATACGGCGACCACCGAGA-3′) Illumina sequencing libraries were then pooled equimolar and subjected to Illumina sequencing on a MiSeq instrument (Illumina, Cat # SY-410-1003) with 300 base paired-end reads using a MiSeq Reagent Kit v3 (Illumina, Cat # MS-102-3003) following the manufacture's recommendations. A minimum of 1000-fold sequence coverage was generated for each locus for at least one treated replicate. PCR, cleanup, pooling and sequencing of treated and untreated samples were performed separately to avoid any possibility of cross contamination between treated and untreated samples or PCR amplicons generated therefrom.

Illumina Sequencing Data QC and Variant Analysis

Using default parameters, the Illumina MiSeq analysis software (MiSeq reporter, version 2.6.2, Illumina) was used to generate amplicon specific FASTQ sequencing data files (Cock et al, Nucleic Acids Res. 2010, 38(6):1767-71, PMID: 20015970). FASTQ files were then processed through an internally developed variant analysis pipeline consisting of a series of public domain software packages joined together using a standard Perl script wrapper. The workflow used was divided into five stages.

Stage 1, PCR Primer and On- and Off-Target Sequence QC:

For both on- and off-target sites the 20 nucleotide gRNA protospacer sequence plus PAM sequence and target specific PCR primer sequences (left and right without the additional Illumina sequences) were aligned to the human genome reference sequence (build GRCh38) using a BLAST search (version 2.2.29+, Altschul et al, J Mol Biol., 1990, 215(3):403-10, PMID: 2231712). On- and off-target sites with multiple genomic locations were flagged.

Stage 2, Sequencer File Decompression:

Illumina sequencer generated FASTQ.GZ files were decompressed to FASTQ files using the gzip script (version 1.3.12) and number of reads per file was calculated. Files with no reads were excluded from further analysis.

Stage 3, Sequence Read Alignment and Quality Trimming:

Sequencing reads in FASTQ files were aligned to the human genome reference sequence (build GRCh38) using the BWA-MEM aligner (version 0.7.4-r385, Li and Durbin, Bioinformatics, 2009, 25(14):1754-60, PMID: 19451168) using ‘hard-clipping’ to trim 3′ ends of reads of Illumina sequences and low quality bases. Resulting aligned reads, in the BAM file format (Li et al, Bioinformatics, 2009 25(16):2078-9, PMID: 19505943), were converted to FASTQ files using the SAMtools script (version 0.1.19-44428cd, Li et al, Bioinformatics, 2009 25(16):2078-9, PMID: 19505943). FASTQ files were then aligned again to the human genome reference sequence (build GRCh38) using the BWA-MEM aligner, this time without ‘hard-clipping’.

Stage 4, Variant (SNP and INDEL) Analysis:

BAM files of aligned reads were processed using the VarDict variant caller (version 1.0 ‘Cas9 aware’ modified by developer ZhangWu Lia, Lai et al, Nucleic Acids Res., 2016, 44(11):e108, PMID: 27060149) with allele frequency detection limit set at >=0.0001 to identify variants (SNPs and INDELs). The Cas9 aware VarDict caller is based on a public domain package but able to move ambiguous variant calls, generated due to repetitive sequences in the alignment region of the variant events, toward the potential Cas9 nuclease cut site in the gRNA protospacer sequence located 3 bases 5′ of the PAM sequence. The SAMtools script was used to calculate read coverage per sample amplicon to determine whether the on- and off-target sites were covered at >1000-fold sequence coverage. Sites with <1000-fold sequence coverage were flagged.

Stage 5, dbSNP Filtering and Treated/Untreated Differential Analysis:

Variants identified were filtered for known variants (SNPs and INDELs) found in dbSNP (build 142, Shery et al, Nucleic Acids Res. 2001, 29(1):308-11, PMID: 11125122). Variants in the treated samples were further filtered to exclude: 1) variants identified in the untreated control samples; 2) variants with a VarDict strand bias of 2:1 (where forward and reverse read counts supporting the reference sequence are balanced but imbalanced for the non-reference variant call); 3) variants located outside a 100 bp window around the potential Cas9 cut site; 4) single nucleotide variants within a 100 bp window around the potential Cas9 cut site. Finally only sites with a combined INDEL frequency of >2% (editing in more than approximately 10-20 cell) in a 100 bp window of the potential Cas9 cut site were considered. Potential active editing sites were further examined at the read alignment level using the Integrative Genome Viewer (IGV version 2.3, Robinson et al, Nat Biotechnol. 2011, 9(1):24-6, PMID: 21221095) that allows for visual inspection of read alignments to the genome reference sequence.

On- and Off-Target Analysis Results

On-target sites for the BCL11A+58 region and the HPFH region gRNAs showed robust editing at the intended Cas9 cut site in treated samples with an INDEL frequency greater than 88% for all gRNAs. Tables 3 and 5 show number of off-target sites characterized in at least one biological replicate. Uncharacterized sites failed PCR primer design or PCR amplification and remain under investigation.

BCL11A+58 Region in Silico Targeted Analysis Results

gRNA CR00309:

The on-target site for gRNA CR00309 showed robust editing at the intended Cas9 cut site with an average INDEL frequency of approximately 92%. Table 31 shows the number of off-target sites characterized. Uncharacterized sites failed in PCR primer design or PCR amplification and remain under investigation. Characterization of potential off-target sites identified four off-target sites in the 100 bp window around the proposed Cas9 cut site in both treated replicates. Site 1 has an average INDEL frequency approximately 18%, has 3 mismatches relative to the on-target gRNA protospacer sequence (5′-CtCaCCtCCACCCTAATCAG-PAM-3′, PAM=AGG) and is located in intron 1 of the Anoctamin 5 gene (ANO5), on chromosome 11 at base pair position 22,195,800-22,195,819, approximately 2.3 kb away from exon 1. Site 2 has an average INDEL frequency of approximately 18%, has 2 mismatches relative to the on-target gRNA protospacer sequence (5′-CACGCCCaCACCtTAATCAG-PAM-3′, PAM=GGG) and is located in an intergenic region of chromosome 12 at base pair position 3,311,901-3,311,926. Site 3 has an average INDEL frequency approximately 80%, has 2 mismatches relative to the on-target gRNA protospacer sequence (5′-CACGaCCCaACCCTAATCAG-PAM-3′, PAM=AGG) and is located in a GenBank (Clark et al., Nucleic Acids Res. 2016 Jan. 4; 44(Database issue): D67-D72, PMID: 26590407) transcript (BC012501 not annotated in RefSeq) on chromosome 1 at base pair position 236,065,415-236,065,434. Site 4 has an average INDEL frequency of approximately 2%, has 4 mismatches relative to the on-target gRNA protospacer sequence (5′-CtaGCCCCtACCCTAATaAG-3′, PAM=TGG) and is located in intron 1 of a GenBank annotated transcript called polyhomeotic 2 protein (not annotated in RefSeq) on chromosome 1 at base pair position 33,412,659-33,412,678.

gRNA CR00311:

The on-target site for gRNA CR00311 showed robust editing at the intended Cas9 cut site with an average INDEL frequency of approximately 95%. Table 31 shows the number of off-target sites successfully characterized. Uncharacterized sites failed in PCR primer design or PCR amplification and remain under investigation. To date no significant off-target activity was observed at sites examined.

gRNA CR000312:

The on-target site for gRNA CR000312 showed robust editing at the intended Cas9 cut site with an average INDEL frequency of approximately 98%. Table 31 shows the number of off-target sites successfully characterized. Uncharacterized sites failed in PCR primer design or PCR amplification and remain under investigation. To date no significant off-target activity was observed at sites examined.

gRNA CR000316:

The on-target site for gRNA CR000316 showed robust editing at the intended Cas9 cut site in with an average INDEL frequency of approximately 91%, however the majority of off-target sites remain to be characterized.

gRNA CR001125:

The on-target site for gRNA CR0001125 showed robust editing at the intended Cas9 cut site with an average INDEL frequency of approximately 91%. Table 31 shows the number of off-target sites successfully characterized. Uncharacterized sites failed in PCR primer design or PCR amplification and remain under investigation. To date no significant off-target activity was observed at sites examined.

gRNA CR001126:

The on-target site for gRNA CR0001126 showed robust editing at the intended Cas9 cut site with an average INDEL frequency of approximately 92%. Table 31 shows the number of off-target sites successfully characterized. Uncharacterized sites failed in PCR primer design or PCR amplification and remain under investigation. Characterization of potential off-target sites identified two off-target sites to date in the 100 bp window around the proposed Cas9 cut site in both treated replicates. The first site has an average INDEL frequency approximately 2%, has 2 mismatches relative to the on-target gRNA protospacer sequence (5′-TTTATaACAGGCTCCAGaAA-PAM-3′, PAM=TGG) and is located in an intergenic region on chromosome 4 at base pair position 35,881,815-35,881,834, approximately 9.5 kb away from the nearest GenBank transcript (not annotated in RefSeq). The second site has an average INDEL frequency of approximately 1.7%, has 4 mismatches relative to the on-target gRNA protospacer sequence (5′ caTATCACAGGCcCCAGGAg-PAM-3′, PAM=GGG) and is located in intron 6 of the Ataxin 1 gene (ATXN1), on chromosome 6 at base pair position 16,519,907-16,519,926, approximately 2.7 kb away from exon 6.

gRNA CR001127:

The on-target site for gRNA CR0001127 showed robust editing at the intended Cas9 cut site with an average INDEL frequency of approximately 97%. Table 31 shows the number of off-target sites successfully characterized. Uncharacterized sites failed in PCR primer design or PCR amplification and remain under investigation. To date no significant off-target activity was observed at sites examined.

gRNA CR001128:

The on-target site for gRNA CR0001128 showed robust editing at the intended Cas9 cut site with an average INDEL frequency of approximately 94%. Table 31 shows the number of off-target sites successfully characterized. Uncharacterized sites failed in PCR primer design or PCR amplification and remain under investigation. To date no significant off-target activity was observed at sites examined.

Manual inspection of all actively edited BCL11 +58 region off-target sites identified showed typical INDEL patterns surrounding the proposed Cas9 cut site typical of Cas9 mediated double stranded break non homologous end joining DNA repair. It is unclear whether editing at the sites identified has any detrimental effect on gene expression or cell viability, further analysis is required.

TABLE 31 Counts of in silico off-target sites identified, sites successfully characterized in at least one treated replicate and sites that show editing for the BCL11A +58 region gRNAs CR00309, CR00311, CR00312, CR00316, CR001125, CR001126, CR001127, and CR001128 are shown. Total Number of in number of silico off- Number in silico target sites of active in silico gRNA name off-target sites characterized off-target sites identified CR00309 141 140 4 CR00311 267 245 0 CR00312 165 163 0 CR00316 346 TBD TBD CR001125 321 319 0 CR001126 349 348 2 CR001127* 367 365 0 CR001128 207 194 0 *only sites with 0-4 nucleotide mismatches were examined.

BCL11A+58 Region GUIDE-Seq Hit Validation Results

Potential off-target hits identified by GUIDE-seq (Tsai et al, Nat Biotechnol. 2015, 33(2):187-97, PMID: 25513782) were characterized in RNP treated and untreated HSPC using targeted sequencing methods described above for in silico defined sites. GUIDE-seq potential hits were identified for gRNAs CR00312, CR00316, CR001125, CR001126, CR001127 and CR001128. No potential hits were identified for gRNA CR00311 and CR001128. When the potential hits were interrogated in HSPCs using targeted sequencing, none of the potential hits validated in treated HSPC for gRNA CR00312, CR001125 and CR001127. One potential hit validated for gRNA CR001126, the same site that was identified by the in silico directed method in intron 6 of ATXN1 (chromosome 6:16,519,907-16,519,926 base pairs).Validation of potential hits for gRNAs CR00309 and CR00316 is still in progress.

HPFH Region in Silico Targeted Analysis Results

gRNA CR001028:

The on-target site for gRNA CR0001028 showed robust editing at the intended Cas9 cut site with an average INDEL frequency of approximately 91%. Table 32 shows the number of off-target sites successfully characterized. Uncharacterized sites failed in PCR primer design or PCR amplification and remain under investigation. Characterization of potential off-target sites identified two off-target sites to date in the 100 bp window around the proposed Cas9 cut site in both treated replicates. Site 1 has an average INDEL frequency approximately 2.8%, has 2 mismatches relative to the on-target gRNA protospacer sequence (5′-TGgGGTGGGGAGATATGaAG-PAM-3′, PAM=AGG) and is located in intron 2 of a non-coding RNA (LF330410, not annotated in RefSeq) located on chromosome 4 at base pair position 58,169,308-58,169,327. Site 2 has an average INDEL frequency approximately 3.5%, has 3 mismatches relative to the on-target gRNA protospacer sequence (5′-gGaGGTGGGGAGAgATGTAG-PAM-3′, PAM=AGG) and is located in intron 1 of the Butyrophilin subfamily 3 member A2 gene (BTN3A2) located on chromosome 6 at base pair position 26,366,733-26,366,752, approximately 1.3 kb from exon 2.

gRNA CR001030:

The on-target site for gRNA CR0001030 showed robust editing at the intended Cas9 cut site with an average INDEL frequency of approximately 89%. Table 32 shows the number of off-target sites successfully characterized. Uncharacterized sites failed in PCR primer design or PCR amplification and remain under investigation. Characterization of potential off-target sites identified one off-target sites to date with average INDEL frequency of 57% in the 100 bp window around the proposed Cas9 cut site in both treated replicates. The site has 3 mismatches relative to the on-target gRNA protospacer sequence (5′-caTGCgGAAAGAGATGCGGT-PAM-3′, PAM=TGG) and is located in exon 4 of the Pyruvate Dehydrogenase Kinase 3 gene (PDK3) located on the X chromosome at base pair position 24,503,476-24,503,495.

gRNA CR001137:

The on-target site for gRNA CR0001037 showed robust editing at the intended Cas9 cut site with an average INDEL frequency of approximately 84%. Table 32 shows the number of off-target sites successfully characterized. Uncharacterized sites failed in PCR primer design or PCR amplification and remain under investigation. To date no significant off-target activity was observed at sites examined.

gRNA CR001221:

The on-target site for gRNA CR0001221 showed robust editing at the intended Cas9 cut site with an average INDEL frequency of approximately 95%. Table 32 shows the number of off-target sites successfully characterized. Uncharacterized sites failed in PCR primer design or PCR amplification and remain under investigation. To date no significant off-target activity was observed at sites examined.

gRNA CR003035:

The on-target site for gRNA CR0003035 showed robust editing at the intended Cas9 cut site with an average INDEL frequency of approximately 89%. Table 32 shows the number of off-target sites successfully characterized. Uncharacterized sites failed in PCR primer design or PCR amplification and remain under investigation. Characterization of potential off-target sites identified two off-target sites to date in the 100 bp window around the proposed Cas9 cut site in both treated replicates. Site 1 has an average INDEL frequency of approximately 20%, has 2 mismatches relative to the on-target gRNA protospacer sequence (5′-AGGtACCTCAaACTCAGCAT-PAM-3′, PAM=AGG) and is located in an intergenic region on chromosome 2 at base pair position 66,281,781-66,281,800 and is approximately 7.1 kb from the nearest transcript (JD432564, not annotated in RefSeq). Site 2 has an average INDEL frequency approximately 2.5%, has 3 mismatches relative to the on-target gRNA protospacer sequence (5′-AGagACCcCAGACTCAGCAT-PAM-3′, PAM=AGG) and is located in an intergenic region on chromosome 10 at base pair position 42,997,289-42,997,308, and is approximately 0.3 kb from MicroRNA 5100 (MIR5100).

gRNA CR003085:

The on-target site for gRNA CR0003038 showed robust editing at the intended Cas9 cut site with an average INDEL frequency of approximately 94%. Table 32 shows the number of off-target sites successfully characterized. Uncharacterized sites failed in PCR primer design or PCR amplification and remain under investigation. Characterization of potential off-target sites identified one off-target sites to date with average INDEL frequency of approximately 2% in the 100 bp window around the proposed Cas9 cut site in both treated replicates. The site has 3 mismatches relative to the on-target gRNA protospacer sequence (5′-ATGGTATGaGAaaTATACTA-PAM-3′, PAM=TGG) and is located in intron 2 of the Solute Carrier Family 25 Member 12 gene (SLC25A12) located on chromosome 2 at base pair position 171,872,630-171,872,649, and is approximately 3.8 kb from exon 3.

Manual inspection of all actively edited HPFH region off-target sites identified showed typical INDEL patterns surrounding the proposed Cas9 cut site typical of Cas9 mediated double stranded break non homologous end joining DNA repair. It is unclear whether editing at the sites identified has any detrimental effect on gene expression or cell viability, further analysis is required.

TABLE 32 Counts of potential in silico off-target sites identified, sites successfully characterized in at least one treated replicate and sites that show editing for the HPFH region gRNAs CR001028, CR001030, CR001137, CR001221, CR003035 and CR003085 are shown. Number of in Total number silico off- Number of of in silico target sites active in silico gRNA name off-target sites characterized off-target sites identified CR001028 233 217 2 CR001030 224 219 1 CR001137 113 109 0 CR001221 229 224 0 CR003035 249 243 2 CR003085 96 95 1

HPFH Region GUIDE-Seq Hit Validation Results

Potential off-target hits identified using GUIDE-seq (Tsai et al, Nat Biotechnol. 2015, 33(2):187-97, PMID: 25513782) were interrogated in RNP treated and untreated HSPC using the same methods described for in silico sites. GUIDE-seq potential off-target hits were identified for gRNA CR001028, CR001030, CR003035 and CR003085 (to date). No hits were identified for gRNAs CR001137 and CR001221 to date. One hit for gRNA CR001028 validated in HSPC, the same site that was identified by the in silico directed method on chromosome 4 at base pair position 58,169,308-58,169,327. One hit validated for gRNA CR001030 in HSPC, the same site that was identified by the in silico directed method in exon 4 of the PDK3 gene. One hit validated for gRNA CR003035 in HSPC, the same site that was identified by the in silico directed method in the intergenic region of chromosome 2 at base pair position 66,281,781-66,281,800. One hit validated for gRNA CR003085 in HSPC, the same site as was identified by the in silico directed method on chromosome 2 at base pair position 171,872,630-171,872,649.

On-Target Analysis for gRNA Editing Efficiency Screening

PCR amplicons targeting the gRNA on-target site were cleaned up using Agencourt AMPure XP beads (Beckman Coulter, Cat # A63882) following the manufacture's recommendations. Samples were quantified using the Quant-iT PicoGreen dsDNA kit (Thermo Fisher, Cat # P7581) using manufacture's recommendations. Amplicons were transformed into Illumina sequencing libraries using the Nextera DNA Library Preparation Kit (Illumina, Cat# FC-121-1031) following the manufacture's recommendations. Resulting sequencing libraries were AMPure bead cleaned up, qPCR quantified, pooled and sequenced with an Illumina MiSeq instrument using 150 base (Illumina, Cat# MS-102-2002) or 250 base (Illumina, Cat# MS-102-2003) paired-end reads as described in the off-target analysis section. For each library a minimum of a 1000-fold sequencing coverage was generated and variants were called using a series of in house scripts. In short, sequencing reads spanning an 80-100 base pair window centered on the gRNA sequence were identified using a string based sequence search, compared to the amplicon sequence, binned by sequence differences and variant frequencies were calculated. Additionally, sequencing reads were aligned to the amplicon sequence using the Illumina MiSeq reporter software (Illumina version 2.6.1) and resulting read alignments were examined using the Integrative Genome Viewer (IGV version 2.3, Robinson et al, Nat Biotechnol. 2011, 9(1):24-6, PMID: 21221095).

Example 10: Evaluation of RNP Concentration On Gene Editing and HbF Induction RNP Dilution Assay to Determine Optimal RNP Concentration for Gene Editing

Gene editing was performed using a serial dilution of Cas9 (iProt: 106331) and guide ribonucleotide complexes (RNP) concentrations (Table 33). Various gRNA used, their formats, and modification applied in this assay are listed in Table 34.

TABLE 33 RNP dilution used to investigate RNP concentration effect on gene editing and HbF induction. RNP RNP RNP RNP RNP gRNA RNP Conc Conc Conc Conc Conc Format Components RNP-1 RNP-2 RNP-3 RNP-4 RNP-5 Single crRNA (ug) 3 1.5 0.75 0.37 0.18 gRNA Cas9 (ug) 3 1.5 0.75 0.37 0.18 RNP (uM) 1.94 0.97 0.48 0.24 0.12 Dual crRNA (ug) 3.86 1.93 0.97 0.48 0.24 gRNA tracrRNA (ug) 3.86 1.93 0.97 0.48 0.24 Cas9 (ug) 3.86 1.93 0.97 0.48 0.24 RNP (uM) 5.89 2.94 1.47 0.74 0.37

TABLE 34 List of gRNAs, in single or dual guide format, with or without chemical modification used in the RNP dilution assay. “OMePS” modification, with respect to dgRNA format, refers to modified crRNA having the following structure: mN*mN*mN*NNNNNNNNNNNNNNNNNGUUUUAGAGCUAUGC UGUU*mU*mU*mG paired with unmodified tracr (i.e., tracrRNA) of SEQ ID NO: 6660; and with respect to sgRNA, refers to a gRNA having the following structure: mN*mN*mN*NNNNNNNNNNNNNNNNNGUUUUAGAGCUAGAAA UAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAA AAGUGGCACCGAGUCGGUGCmU*mU*mU*U, where N = a nucleotide of the targeting domain, mN refers to a 2′-OMe-modified nucelotide, and * refers to a phosphorothioate bond. “Unmodified” refers to a gRNA having no RNA modifications: dgRNA consist of NNNNNNNNNNNNN NNNNNNNGUUUUAGAGCUAUGCUGUUUUG paired with SEQ ID NO: 6660; sgRNA refer to NNNNNNNNNNNNNNNNNNNNGUUUUAGAGCUAGAAAUAGCA AGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUG GCACCGAGUCGGUGCUUUU, where N = the nucleotides of the indicated targeting domain gRNA gRNA Targeting Format Sample ID Domain ID gRNA Modification Dual gRNA 1 CR00312 Unmodified 2 CR001128 Unmodified 3 CR00312 OMePS 4 CR001128 OMePS Single gRNA 5 CR00312 Unmodified 6 CR001128 Unmodified 7 CR00312 OMePS 8 CR001128 OMePS 9 Mock electroporation N/A control

CD34+ cells were electroporated as described previously, and subjected to measurement of cell viability, gene editing efficiency, and ability to produce HbF. When assessing cell viability, the results showed that varying RNP concentration had no impact on cell viability upon electroporation, either when single or dual guide format is used (FIG. 39A and FIG. 39B). Upon gene editing of CD34+ cells, NGS data showed that RNP concentrations down to 1.47 uM achieved maximum % gene editing efficiency for unmodified CR00312 and CR001128, and modified CR00312, while maximum % gene editing efficiency for modified CR001228 was achieved at RNP concentrations as low as 2.94 uM (FIG. 40A). For sgRNA formats, all gRNAs tested achieved maximum % editing at RNP concentrations down to 0.48 uM (FIG. 40B). In measuring the ability of gene edited cells to differentiate into erythroid lineage and produce HbF, our data showed that the RNP concentration down to 2.94 uM for dgRNA-containing RNP (FIG. 41A) and down to 0.97 uM for sgRNA-containing RNP (FIG. 41B) resulted in maximum levels of HbF induction.

This application is being filed with a sequence listing. To the extent there are any discrepancies between the sequence listing and any sequence recited in the specification, the sequence recited in the specification should be considered the correct sequence. Unless otherwise indicated, all genomic locations are according to hg38.

INCORPORATION BY REFERENCE

All publications, patents, and patent applications mentioned herein are hereby incorporated by reference in their entirety as if each individual publication, patent or patent application was specifically and individually indicated to be incorporated by reference. In case of conflict, the present application, including any definitions herein, will control.

EQUIVALENTS

Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. While this invention has been disclosed with reference to specific aspects, it is apparent that other aspects and variations of this invention may be devised by others skilled in the art without departing from the true spirit and scope of the invention. The appended claims are intended to be construed to include all such aspects and equivalent variations. 

1. A gRNA molecule comprising a tracr and crRNA, wherein the crRNA comprises a targeting domain that is complementary with a target sequence of a BCL11A gene (e.g., a human BCL11a gene), a BCL11a enhancer (e.g., a human BCL11a enhancer), or a HFPH region (e.g., a human HPFH region).
 2. A gRNA molecule of claim 1, wherein the target sequence is of the BCL11A gene, and the targeting domain comprises, e.g., consists of, any one of SEQ ID NO: 1 to SEQ ID NO: 85 or SEQ ID NO: 400 to SEQ ID NO:
 1231. 3. A gRNA molecule of claim 1, wherein the target sequence is of a BCL11a enhancer, and the targeting domain comprises, e.g., consists of, any one of SEQ ID NO: 1232 to SEQ ID NO:
 1499. 4. A gRNA molecule of claim 1, wherein the target sequence is of a BCL11a enhancer, and the targeting domain comprises, e.g., consists of, any one of SEQ ID NO: 182 to SEQ ID NO: 277 or SEQ ID NO: 334 to SEQ ID NO:
 341. 5. A gRNA molecule of claim 4, wherein the targeting domain comprises, e.g., consists of, any one of SEQ ID NO: 341, SEQ ID NO: 246, SEQ ID NO: 248, SEQ ID NO: 247, SEQ ID NO: 245, SEQ ID NO: 249, SEQ ID NO: 244, SEQ ID NO: 199, SEQ ID NO: 251, SEQ ID NO: 250, SEQ ID NO: 334, SEQ ID NO: 185, SEQ ID NO: 186, SEQ ID NO: 336, or SEQ ID NO:
 337. 6. A gRNA molecule of claim 4, wherein the targeting domain comprises, e.g., consists of, any one of SEQ ID NO: 247, SEQ ID NO: 248, SEQ ID NO: 335, SEQ ID NO: 336, SEQ ID NO: 337, or SEQ ID NO:
 338. 7. A gRNA molecule of claim 4, wherein the targeting domain comprises, e.g., consists of, any one of SEQ ID NO: 248 or SEQ ID NO:
 338. 8. A gRNA molecule of claim 4, wherein the targeting domain comprises, e.g., consists of, SEQ ID NO:
 248. 9. A gRNA molecule of claim 4, wherein the targeting domain comprises, e.g., consists of, SEQ ID NO:
 338. 10. A gRNA molecule of claim 1, wherein the target sequence is of a BCL11a enhancer, and the targeting domain comprises, e.g., consists of, any one of SEQ ID NO: 278 to SEQ ID NO:
 333. 11. A gRNA molecule of claim 10, wherein the targeting domain comprises, e.g., consists of, any one of SEQ ID NO: 318, SEQ ID NO: 312, SEQ ID NO: 313, SEQ ID NO: 294, SEQ ID NO: 310, SEQ ID NO: 319, SEQ ID NO: 298, SEQ ID NO: 322, SEQ ID NO: 311, SEQ ID NO: 315, SEQ ID NO: 290, SEQ ID NO: 317, SEQ ID NO: 309, SEQ ID NO: 289, or SEQ ID NO:
 281. 12. A gRNA molecule of claim 10, wherein the targeting domain comprises, e.g., consists of, SEQ ID NO:
 318. 13. A gRNA molecule of claim 1, wherein the target sequence is of a BCL11a enhancer, and the targeting domain comprises, e.g., consists of, any one of SEQ ID NO: 1596 to SEQ ID NO:
 1691. 14. A gRNA molecule of claim 13, wherein the targeting domain comprises, e.g., consists of, any one of SEQ ID NO: 1683, SEQ ID NO: 1638, SEQ ID NO: 1647, SEQ ID NO: 1609, SEQ ID NO: 1621, SEQ ID NO: 1617, SEQ ID NO: 1654, SEQ ID NO: 1631, SEQ ID NO: 1620, SEQ ID NO: 1637, SEQ ID NO: 1612, SEQ ID NO: 1656, SEQ ID NO: 1619, SEQ ID NO: 1675, SEQ ID NO: 1645, SEQ ID NO: 1598, SEQ ID NO: 1599, SEQ ID NO: 1663, SEQ ID NO: 1677, or SEQ ID NO:
 1626. 15. A gRNA molecule of claim 1, wherein the target sequence is of a HFPH region (e.g., a French HPFH region), and the targeting domain comprises, e.g., consists of, any one of SEQ ID NO: 86 to SEQ ID NO: 181, SEQ ID NO: 1500 to SEQ ID NO: 1595, or SEQ ID NO: 1692 to SEQ ID NO:
 1761. 16. A gRNA molecule of claim 15, wherein the targeting domain comprises, e.g., consists of, any one of SEQ ID NO: 100, SEQ ID NO: 165, SEQ ID NO: 113, SEQ ID NO: 99, SEQ ID NO: 112, SEQ ID NO: 98, SEQ ID NO: 1580, SEQ ID NO: 106, SEQ ID NO: 1503, SEQ ID NO: 1589, SEQ ID NO: 160, SEQ ID NO: 1537, SEQ ID NO: 159, SEQ ID NO: 101, SEQ ID NO: 162, SEQ ID NO: 104, SEQ ID NO: 138, SEQ ID NO: 1536, SEQ ID NO: 1539, SEQ ID NO:
 1585. 17. A gRNA molecule of claim 15, wherein the targeting domain comprises, e.g., consists of, any one of SEQ ID NO: 98, SEQ ID NO: 100, SEQ ID NO: 1505, SEQ ID NO: 1589, SEQ ID NO: 1700, or SEQ ID NO:
 1750. 18. A gRNA molecule of claim 15, wherein the targeting domain comprises, e.g., consists of, any one of SEQ ID NO: 100, SEQ ID NO: 165, or SEQ ID NO:
 113. 19. The gRNA molecule of any of claims 2-18, wherein the targeting domain comprises, e.g., consists of, 17, 18, 19, 20, 21, 22, 23, or 24 consecutive nucleic acids of any one of the recited targeting domain sequences.
 20. The gRNA molecule of claim 16, wherein the 17, 18, 19, 20, 21, 22, 23, or 24 consecutive nucleic acids of any one of the recited targeting domain sequences are the 17, 18, 19, 20, 21, 22, 23, or 24 consecutive nucleic acids disposed at the 3′ end of the recited targeting domain sequence.
 21. The gRNA molecule of claim 16, wherein the 17, 18, 19, 20, 21, 22, 23, or 24 consecutive nucleic acids of any one of the recited targeting domain sequences are the 17, 18, 19, 20, 21, 22, 23, or 24 consecutive nucleic acids disposed at the 5′ end of the recited targeting domain sequence.
 22. The gRNA molecule of claim 16, wherein the 17, 18, 19, 20, 21, 22, 23, or 24 consecutive nucleic acids of any one of the recited targeting domain sequences do not comprise either the 5′ or 3′ nucleic acid of the recited targeting domain sequence.
 23. The gRNA molecule of any of claims 2-22, wherein the targeting domain consists of the recited targeting domain sequence.
 24. The gRNA molecule of any of the previous claims, wherein a portion of the crRNA and a portion of the tracr hybridize to form a flagpole comprising SEQ ID NO: 6584 or
 6585. 25. The gRNA molecule of claim 24, wherein the flagpole further comprises a first flagpole extension, located 3′ to the crRNA portion of the flagpole, wherein said first flagpole extension comprises SEQ ID NO:
 6586. 26. The gRNA molecule of claim 24 or 25, wherein the flagpole further comprises a second flagpole extension located 3′ to the crRNA portion of the flagpole and, if present, the first flagpole extension, wherein said second flagpole extension comprises SEQ ID NO:
 6587. 27. The gRNA molecule of any of claims 1-26, wherein the tracr comprises SEQ ID NO: 6660 or SEQ ID NO:
 6661. 28. The gRNA molecule of any of claims 1-26, wherein the tracr comprises SEQ ID NO: 7812, optionally further comprising, at the 3′ end, an additional 1, 2, 3, 4, 5, 6, or 7 uracil (U) nucleotides.
 29. The gRNA molecule of any of claims 1-28, wherein the crRNA comprises, from 5′ to 3′, [targeting domain]-: a) SEQ ID NO: 6584; b) SEQ ID NO: 6585; c) SEQ ID NO: 6605; d) SEQ ID NO: 6606; e) SEQ ID NO: 6607; f) SEQ ID NO: 6608; or g) SEQ ID NO:
 7806. 30. The gRNA molecule of any of claim 1-23 or 29, wherein the tracr comprises, from 5′ to 3′: a) SEQ ID NO: 6589; b) SEQ ID NO: 6590; c) SEQ ID NO: 6609; d) SEQ ID NO: 6610; e) SEQ ID NO: 6660; f) SEQ ID NO: 6661; g) SEQ ID NO: 7812; h) SEQ ID NO: 7807; i) (SEQ ID NO: 7808; j) SEQ ID NO: 7809; k) any of a) to j), above, further comprising, at the 3′ end, at least 1, 2, 3, 4, 5, 6 or 7 uracil (U) nucleotides, e.g., 1, 2, 3, 4, 5, 6, or 7 uracil (U) nucleotides; l) any of a) to k), above, further comprising, at the 3′ end, at least 1, 2, 3, 4, 5, 6 or 7 adenine (A) nucleotides, e.g., 1, 2, 3, 4, 5, 6, or 7 adenine (A) nucleotides; or m) any of a) to l), above, further comprising, at the 5′ end (e.g., at the 5′ terminus), at least 1, 2, 3, 4, 5, 6 or 7 adenine (A) nucleotides, e.g., 1, 2, 3, 4, 5, 6, or 7 adenine (A) nucleotides.
 31. The gRNA molecule of any of claims 1-23, wherein the targeting domain and the tracr are disposed on separate nucleic acid molecules, and wherein the nucleic acid molecule comprising the targeting domain comprises SEQ ID NO: 6607, optionally disposed immediately 3′ to the targeting domain, and the nucleic acid molecule comprising the tracr comprises, e.g., consists of, SEQ ID NO:
 6660. 32. The gRNA molecule of any of claims 27-28, wherein the crRNA portion of the flagpole comprises SEQ ID NO: 6607 or SEQ ID NO:
 6608. 33. The gRNA molecule of any of claims 1-26, wherein the tracr comprises SEQ ID NO: 6589 or 6590, and optionally, if a first flagpole extension is present, a first tracr extension, disposed 5′ to SEQ ID NO: 6589 or 6590, said first tracr extension comprising SEQ ID NO:
 6591. 34. The gRNA molecule of any of claims 1-33, wherein the targeting domain and the tracr are disposed on separate nucleic acid molecules.
 35. The gRNA molecule of any of claims 1-33, wherein the targeting domain and the tracr are disposed on a single nucleic acid molecule, and wherein the tracr is disposed 3′ to the targeting domain.
 36. The gRNA molecule of claim 35, further comprising a loop, disposed 3′ to the targeting domain and 5′ to the tracr.
 37. The gRNA molecule of claim 36, wherein the loop comprises SEQ ID NO:
 6588. 38. The gRNA molecule of any of claims 1-23, comprising, from 5′ to 3′, [targeting domain]-: (a) SEQ ID NO: 6601; (b) SEQ ID NO: 6602; (c) SEQ ID NO: 6603; (d) SEQ ID NO: 6604; (e) SEQ ID NO: 7811; or (f) any of (a) to (e), above, further comprising, at the 3′ end, 1, 2, 3, 4, 5, 6 or 7 uracil (U) nucleotides.
 39. The gRNA molecule of any of claims 1-40, wherein the targeting domain and the tracr are disposed on a single nucleic acid molecule, and wherein said nucleic acid molecule comprises, e.g., consists of, said targeting domain and SEQ ID NO: 7811, optionally disposed immediately 3′ to said targeting domain.
 40. The gRNA molecule of any of claims 1-39 wherein one, or optionally more than one, of the nucleic acid molecules comprising the gRNA molecule comprises: a) one or more, e.g., three, phosphorothioate modifications at the 3′ end of said nucleic acid molecule or molecules; b) one or more, e.g., three, phosphorothioate modifications at the 5′ end of said nucleic acid molecule or molecules; c) one or more, e.g., three, 2′-O-methyl modifications at the 3′ end of said nucleic acid molecule or molecules; d) one or more, e.g., three, 2′-O-methyl modifications at the 5′ end of said nucleic acid molecule or molecules; e) a 2′ O-methyl modification at each of the 4^(th)-to-terminal, 3^(rd)-to-terminal, and 2^(nd)-to-terminal 3′ residues of said nucleic acid molecule or molecules; f) a 2′ O-methyl modification at each of the 4^(th)-to-terminal, 3^(rd)-to-terminal, and 2^(nd)-to-terminal 5′ residues of said nucleic acid molecule or molecules; or f) any combination thereof.
 41. A gRNA molecule of claim 1, comprising, e.g., consisting of, the sequence: (a) SEQ ID NO: 342; (b) SEQ ID NO: 343; or (c) SEQ ID NO:
 1762. 42. A gRNA molecule of claim 1, comprising, e.g., consisting of: (a) a crRNA comprising, e.g., consisting of, SEQ ID NO: 344, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA comprising, e.g., consisting of, SEQ ID NO: 344, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA comprising, e.g., consisting of, SEQ ID NO: 345, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA comprising, e.g., consisting of, SEQ ID NO: 345, and a tracr comprising, e.g., consisting of, SEQ ID NO:
 346. 43. A gRNA molecule of claim 1, comprising, e.g., consisting of, the sequence: (a) SEQ ID NO: 347; (b) SEQ ID NO: 348; or (c) SEQ ID NO:
 1763. 44. A gRNA molecule of claim 1, comprising, e.g., consisting of: (a) a crRNA comprising, e.g., consisting of, SEQ ID NO: 349, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA comprising, e.g., consisting of, SEQ ID NO: 349, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA comprising, e.g., consisting of, SEQ ID NO: 350, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA comprising, e.g., consisting of, SEQ ID NO: 350, and a tracr comprising, e.g., consisting of, SEQ ID NO:
 346. 45. A gRNA molecule of claim 1, comprising, e.g., consisting of, the sequence: (a) SEQ ID NO: 351; (b) SEQ ID NO: 352; or (c) SEQ ID NO:
 1764. 46. A gRNA molecule of claim 1, comprising, e.g., consisting of: (a) a crRNA comprising, e.g., consisting of, SEQ ID NO: 353, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA comprising, e.g., consisting of, SEQ ID NO: 353, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA comprising, e.g., consisting of, SEQ ID NO: 354, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA comprising, e.g., consisting of, SEQ ID NO: 354, and a tracr comprising, e.g., consisting of, SEQ ID NO:
 346. 47. A gRNA molecule of claim 1, comprising, e.g., consisting of, the sequence: (a) SEQ ID NO: 355; (b) SEQ ID NO: 356; or (c) SEQ ID NO:
 1765. 48. A gRNA molecule of claim 1, comprising, e.g., consisting of: (a) a crRNA comprising, e.g., consisting of, SEQ ID NO: 357, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA comprising, e.g., consisting of, SEQ ID NO: 357, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA comprising, e.g., consisting of, SEQ ID NO: 358, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA comprising, e.g., consisting of, SEQ ID NO: 358, and a tracr comprising, e.g., consisting of, SEQ ID NO:
 346. 49. A gRNA molecule of claim 1, comprising, e.g., consisting of, the sequence: (a) SEQ ID NO: 359; (b) SEQ ID NO: 360; or (c) SEQ ID NO:
 1766. 50. A gRNA molecule of claim 1, comprising, e.g., consisting of: (a) a crRNA comprising, e.g., consisting of, SEQ ID NO: 361, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA comprising, e.g., consisting of, SEQ ID NO: 361, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA comprising, e.g., consisting of, SEQ ID NO: 362, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA comprising, e.g., consisting of, SEQ ID NO: 362, and a tracr comprising, e.g., consisting of, SEQ ID NO:
 346. 51. A gRNA molecule of claim 1, comprising, e.g., consisting of, the sequence: (a) SEQ ID NO: 363; (b) SEQ ID NO: 364; or (c) SEQ ID NO:
 1767. 52. A gRNA molecule of claim 1, comprising, e.g., consisting of: (a) a crRNA comprising, e.g., consisting of, SEQ ID NO: 365, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA comprising, e.g., consisting of, SEQ ID NO: 365, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA comprising, e.g., consisting of, SEQ ID NO: 366, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA comprising, e.g., consisting of, SEQ ID NO: 366, and a tracr comprising, e.g., consisting of, SEQ ID NO:
 346. 53. A gRNA molecule of claim 1, comprising, e.g., consisting of, the sequence: (a) SEQ ID NO: 367; (b) SEQ ID NO: 368; or (c) SEQ ID NO:
 1768. 54. A gRNA molecule of claim 1, comprising, e.g., consisting of: (a) a crRNA comprising, e.g., consisting of, SEQ ID NO: 369, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA comprising, e.g., consisting of, SEQ ID NO: 369, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA comprising, e.g., consisting of, SEQ ID NO: 370, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA comprising, e.g., consisting of, SEQ ID NO: 370, and a tracr comprising, e.g., consisting of, SEQ ID NO:
 346. 55. A gRNA molecule of claim 1, comprising, e.g., consisting of, the sequence: (a) SEQ ID NO: 371; (b) SEQ ID NO: 372; or (c) SEQ ID NO:
 1769. 56. A gRNA molecule of claim 1, comprising, e.g., consisting of: (a) a crRNA comprising, e.g., consisting of, SEQ ID NO: 373, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA comprising, e.g., consisting of, SEQ ID NO: 373, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA comprising, e.g., consisting of, SEQ ID NO: 374, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA comprising, e.g., consisting of, SEQ ID NO: 374, and a tracr comprising, e.g., consisting of, SEQ ID NO:
 346. 57. A gRNA molecule of claim 1, comprising, e.g., consisting of, the sequence: (a) SEQ ID NO: 375; (b) SEQ ID NO: 376; or (c) SEQ ID NO:
 1770. 58. A gRNA molecule of claim 1, comprising, e.g., consisting of: (a) a crRNA comprising, e.g., consisting of, SEQ ID NO: 377, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA comprising, e.g., consisting of, SEQ ID NO: 377, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA comprising, e.g., consisting of, SEQ ID NO: 378, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA comprising, e.g., consisting of, SEQ ID NO: 378, and a tracr comprising, e.g., consisting of, SEQ ID NO:
 346. 59. A gRNA molecule of claim 1, comprising, e.g., consisting of, the sequence: (a) SEQ ID NO: 379; (b) SEQ ID NO: 380; or (c) SEQ ID NO:
 1771. 60. A gRNA molecule of claim 1, comprising, e.g., consisting of: (a) a crRNA comprising, e.g., consisting of, SEQ ID NO: 381, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA comprising, e.g., consisting of, SEQ ID NO: 381, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA comprising, e.g., consisting of, SEQ ID NO: 382, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA comprising, e.g., consisting of, SEQ ID NO: 382, and a tracr comprising, e.g., consisting of, SEQ ID NO:
 346. 61. A gRNA molecule of claim 1, comprising, e.g., consisting of, the sequence: (a) SEQ ID NO: 383; (b) SEQ ID NO: 384; or (c) SEQ ID NO:
 1772. 62. A gRNA molecule of claim 1, comprising, e.g., consisting of: (a) a crRNA comprising, e.g., consisting of, SEQ ID NO: 385, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA comprising, e.g., consisting of, SEQ ID NO: 385, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA comprising, e.g., consisting of, SEQ ID NO: 386, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA comprising, e.g., consisting of, SEQ ID NO: 386, and a tracr comprising, e.g., consisting of, SEQ ID NO:
 346. 63. A gRNA molecule of claim 1, comprising, e.g., consisting of, the sequence: (a) SEQ ID NO: 387; (b) SEQ ID NO: 388; or (c) SEQ ID NO:
 1773. 64. A gRNA molecule of claim 1, comprising, e.g., consisting of: (a) a crRNA comprising, e.g., consisting of, SEQ ID NO: 389, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA comprising, e.g., consisting of, SEQ ID NO: 389, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA comprising, e.g., consisting of, SEQ ID NO: 390, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA comprising, e.g., consisting of, SEQ ID NO: 390, and a tracr comprising, e.g., consisting of, SEQ ID NO:
 346. 65. A gRNA molecule of claim 1, comprising, e.g., consisting of, the sequence: (a) SEQ ID NO: 391; (b) SEQ ID NO: 392; or (c) SEQ ID NO:
 1774. 66. A gRNA molecule of claim 1, comprising, e.g., consisting of: (a) a crRNA comprising, e.g., consisting of, SEQ ID NO: 393, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA comprising, e.g., consisting of, SEQ ID NO: 393, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA comprising, e.g., consisting of, SEQ ID NO: 394, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA comprising, e.g., consisting of, SEQ ID NO: 394, and a tracr comprising, e.g., consisting of, SEQ ID NO:
 346. 67. A gRNA molecule of claim 1, comprising, e.g., consisting of, the sequence: (a) SEQ ID NO: 395; (b) SEQ ID NO: 396; or (c) SEQ ID NO:
 1775. 68. A gRNA molecule of claim 1, comprising, e.g., consisting of: (a) a crRNA comprising, e.g., consisting of, SEQ ID NO: 397, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; (b) a crRNA comprising, e.g., consisting of, SEQ ID NO: 397, and a tracr comprising, e.g., consisting of, SEQ ID NO: 346; (c) a crRNA comprising, e.g., consisting of, SEQ ID NO: 398, and a tracr comprising, e.g., consisting of, SEQ ID NO: 6660; or (d) a crRNA comprising, e.g., consisting of, SEQ ID NO: 398, and a tracr comprising, e.g., consisting of, SEQ ID NO:
 346. 69. A gRNA molecule of any of claims 1-68, wherein when a CRISPR system (e.g., an RNP as described herein) comprising the gRNA molecule is introduced into a cell, an indel is formed at or near the target sequence complementary to the targeting domain of the gRNA molecule.
 70. The gRNA molecule of claim 69, wherein the indel does not comprise a nucleotide of a GATA-1 or TAL-1 binding site.
 71. A gRNA molecule of any of claims 1-70, wherein when a CRISPR system (e.g., an RNP as described herein) comprising the gRNA molecule is introduced into a population of cells, an indel is formed at or near the target sequence complementary to the targeting domain of the gRNA molecule in at least about 40%, e.g., at least about 50%, e.g., at least about 60%, e.g., at least about 70%, e.g., at least about 80%, e.g., at least about 90%, e.g., at least about 95%, e.g., at least about 96%, e.g., at least about 97%, e.g., at least about 98%, e.g., at least about 99%, of the cells of the population.
 72. A gRNA molecule of any of claims 1-68, wherein when a CRISPR system (e.g., an RNP as described herein) comprising the gRNA molecule is introduced into a population of cells, an indel that does not comprise a nucleotide of a GATA-1 or TAL-1 binding site is formed at or near the target sequence complementary to the targeting domain of the gRNA molecule in at least about 20%, e.g., at least about 30%, e.g., at least about 35%, e.g., at least about 40%, e.g., at least about 45%, e.g., at least about 50%, e.g., at least about 55%, e.g., at least about 60%, e.g., at least about 65%, e.g., at least about 70%, e.g., at least about 75%, e.g., at least about 80%, e.g., at least about 85%, e.g., at least about 90%, e.g., at least about 95%, e.g., at least about 99%, of the cells of the population.
 73. The gRNA molecule of any of claims 71-72, wherein in at least about 30%, e.g., least about 40%, e.g., at least about 50%, e.g., at least about 60%, e.g., at least about 70%, e.g., at least about 80%, e.g., at least about 90%, e.g., at least about 95%, e.g., at least about 96%, e.g., at least about 97%, e.g., at least about 98%, e.g., at least about 99%, of the cells of the population, the indel is an indel listed in any of FIG. 25, Table 15, Table 26, Table 27 or Table
 37. 74. The gRNA molecule of any of claims 71-73, wherein the three most frequently detected indels in said population of cells comprise the indels associated with any gRNA molecule listed in any of FIG. 25, Table 15, Table 26, Table 27 or Table
 37. 75. The gRNA molecule of any of claims 69-74, wherein the indel is as measured by next generation sequencing (NGS).
 76. A gRNA molecule of any of claims 1-75, wherein when a CRISPR system (e.g., an RNP as described herein) comprising the gRNA molecule is introduced into a cell, expression of fetal hemoglobin is increased in said cell or its progeny, e.g., its erythroid progeny, e.g., its red blood cell progeny.
 77. A gRNA molecule of claim 76, wherein expression of fetal hemoglobin is increased in said cell or its progeny, e.g., its erythroid progeny, e.g., its red blood cell progeny, by at least about 20%, e.g., at least about 30%, e.g., at least about 40%, e.g., at least about 50%, e.g., at least about 60%, e.g., at least about 70%, e.g., at least about 80%, e.g., at least about 90%, e.g., at least about 95%, e.g., at least about 96%, e.g., at least about 97%, e.g., at least about 98%, e.g., at least about 99%.
 78. A gRNA molecule of any of claims 76-77, wherein said cell or its progeny, e.g., its erythroid progeny, e.g., its red blood cell progeny, produces at least about 6 picograms (e.g., at least about 7 picograms, at least about 8 picograms, at least about 9 picograms, at least about 10 picograms, or from about 8 to about 9 picograms, or from about 9 to about 10 picograms) fetal hemoglobin per cell.
 79. The gRNA molecule of any of claims 1-78, wherein when a CRISPR system (e.g., an RNP as described herein) comprising the gRNA molecule is introduced into a cell, no off-target indels are formed in said cell, e.g., as detectible by next generation sequencing and/or a nucleotide insertional assay.
 80. The gRNA molecule of any of claims 1-78, wherein when a CRISPR system (e.g., an RNP as described herein) comprising the gRNA molecule is introduced into a population of cells, no off-target indel is detected in more than about 5%, e.g., more than about 1%, e.g., more than about 0.1%, e.g., more than about 0.01%, of the cells of the population of cells, e.g., as detectible by next generation sequencing and/or a nucleotide insertional assay.
 81. The gRNA molecule of any of claims 69-80, wherein the cell is (or population of cells comprises) a mammalian, primate, or human cell, e.g., is a human cell.
 82. The gRNA molecule of claim 81, wherein the cell is (or population of cells comprises) an HSPC.
 83. The gRNA molecule of claim 82, wherein the HSPC is CD34+.
 84. The gRNA molecule of claim 83, wherein the HSPC is CD34+CD90+.
 85. The gRNA molecule of any of claims 69-84, wherein the cell is autologous with respect to a patient to be administered said cell.
 86. The gRNA molecule of any of claims 69-84, wherein the cell is allogeneic with respect to a patient to be administered said cell.
 87. A composition comprising: 1) one or more gRNA molecules (including a first gRNA molecule) of any of claims 1-86 and a Cas9 molecule; 2) one or more gRNA molecules (including a first gRNA molecule) of any of claims 1-86 and nucleic acid encoding a Cas9 molecule; 3) nucleic acid encoding one or more gRNA molecules (including a first gRNA molecule) of any of claims 1-86 and a Cas9 molecule; 4) nucleic acid encoding one or more gRNA molecules (including a first gRNA molecule) of any of claims 1-86 and nucleic acid encoding a Cas9 molecule; or 5) any of 1) to 4), above, and a template nucleic acid; or 6) any of 1) to 4) above, and nucleic acid comprising sequence encoding a template nucleic acid.
 88. A composition comprising a first gRNA molecule of any of claims 1-86, further comprising a Cas9 molecule.
 89. The composition of claim 87 or 88, wherein the Cas9 molecule is an active or inactive s. pyogenes Cas9.
 90. The composition of claim 87-89, wherein the Cas9 molecule comprises SEQ ID NO:
 6611. 91. The composition of claim 87-89, wherein the Cas9 molecule comprises, e.g., consists of: (a) SEQ ID NO: 7821; (b) SEQ ID NO: 7822; (c) SEQ ID NO: 7823; (d) SEQ ID NO: 7824; (e) SEQ ID NO: 7825; (f) SEQ ID NO: 7826; (g) SEQ ID NO: 7827; (h) SEQ ID NO: 7828; (i) SEQ ID NO: 7829; (j) SEQ ID NO: 7830; or (k) SEQ ID NO:
 7831. 92. The composition of any of claims 88-91, wherein the first gRNA molecule and Cas9 molecule are present in a ribonuclear protein complex (RNP).
 93. The composition of any of claims 87-92, further comprising a second gRNA molecule; a second gRNA molecule and a third gRNA molecule; or a second gRNA molecule, optionally, a third gRNA molecule, and, optionally, a fourth gRNA molecule, wherein the second gRNA molecule, the optional third gRNA molecule, and the optional fourth gRNA molecule are a gRNA molecule of any of claims 1-68, and wherein each gRNA molecule of the composition is complementary to a different target sequence.
 94. The composition of claim 93, wherein two or more of the first gRNA molecule, the second gRNA molecule, the optional third gRNA molecule, and the optional fourth gRNA molecule are complementary to target sequences within the same gene or region.
 95. The composition of claim 93 or 94, wherein the first gRNA molecule, the second gRNA molecule, the optional third gRNA molecule, and the optional fourth gRNA molecule are complementary to target sequences not more than 20000 nucleotides, not more than 10000 nucleotides, not more than 6000, not more than 5000 nucleotides, not more than 4000, not more than 1000 nucleotides, not more than 500 nucleotides, not more than 400 nucleotides, not more than 300 nucleotides, not more than 200 nucleotides, not more than 100 nucleotides, not more than 90 nucleotides, not more than 80 nucleotides, not more than 70 nucleotides, not more than 60 nucleotides, not more than 50 nucleotides, not more than 40 nucleotides, not more than 30 nucleotides, not more than 20 nucleotides or not more than 10 nucleotides apart.
 96. The composition of claim 93, wherein two or more of the first gRNA molecule, the second gRNA molecule, the optional third gRNA molecule, and the optional fourth gRNA molecule are complementary to target sequence within different genes or regions.
 97. The composition of any of claims 94-95, comprising a first gRNA molecule and a second gRNA molecule, wherein the first gRNA molecule and second gRNA molecule are: (a) independently selected from the gRNA molecules of claim 4, and are complementary to different target sequences; (b) independently selected from the gRNA molecules of claim 5, and are complementary to different target sequences; c) independently selected from the gRNA molecules of claim 6, and are complementary to different target sequences; or (d) independently selected from the gRNA molecules of claim 7, and are complementary to different target sequences; or (e) independently selected from the gRNA molecules of any of claims 41-56, and are complementary to different target sequences.
 98. The composition of any of claims 94-95, comprising a first gRNA molecule and a second gRNA molecule, wherein the first gRNA molecule and second gRNA molecule are: (a) independently selected from the gRNA molecules of claim 10, and are complementary to different target sequences; or (b) independently selected from the gRNA molecules of claim 11, and are complementary to different target sequences.
 99. The composition of any of claims 94-95, comprising a first gRNA molecule and a second gRNA molecule, wherein the first gRNA molecule and second gRNA molecule are: (a) independently selected from the gRNA molecules of claim 13, and are complementary to different target sequences; or (b) independently selected from the gRNA molecules of claim 14, and are complementary to different target sequences.
 100. The composition of any of claims 94-96, comprising a first gRNA molecule and a second gRNA molecule, wherein the first gRNA molecule and second gRNA molecule are: (a) independently selected from the gRNA molecules of claim 16, and are complementary to different target sequences; (b) independently selected from the gRNA molecules of claim 17, and are complementary to different target sequences; (c) independently selected from the gRNA molecules of claim 18, and are complementary to different target sequences; or (d) independently selected from the gRNA molecules of any of claims 57-68, and are complementary to different target sequences.
 101. The composition of any of claims 94-96, comprising a first gRNA molecule and a second gRNA molecule, wherein: (1) the first gRNA molecule is: (a) selected from the gRNA molecules of claim 4, (b) selected from the gRNA molecules of claim 5, (c) selected from the gRNA molecules of claim 6, (d) selected from the gRNA molecules of claim 7, or (e) selected from the gRNA molecules of any of claims 41-56; and (2) the second gRNA molecule is: (a) selected from the gRNA molecules of claim 10, or (b) selected from the gRNA molecules of claim
 11. 102. The composition of any of claims 94-96, comprising a first gRNA molecule and a second gRNA molecule, wherein: (1) the first gRNA molecule is: (a) selected from the gRNA molecules of claim 4, (b) selected from the gRNA molecules of claim 5, (c) selected from the gRNA molecules of claim 6, (d) selected from the gRNA molecules of claim 7, or (e) selected from the gRNA molecules of any of claims 41-56; and (2) the second gRNA molecule is: (a) selected from the gRNA molecules of claim 13, (b) selected from the gRNA molecules of claim
 14. 103. The composition of any of claims 94-96, comprising a first gRNA molecule and a second gRNA molecule, wherein: (1) the first gRNA molecule is: (a) selected from the gRNA molecules of claim 4, (b) selected from the gRNA molecules of claim 5, (c) selected from the gRNA molecules of claim 6, (d) selected from the gRNA molecules of claim 7, or (e) selected from the gRNA molecules of any of claims 41-56; and (2) the second gRNA molecule is: (a) selected from the gRNA molecules of claim 16, (b) selected from the gRNA molecules of claim 17, (c) selected from the gRNA molecules of claim 18, or (d) selected from the gRNA molecules of any of claims 57-68.
 104. The composition of any of claims 94-96, comprising a first gRNA molecule and a second gRNA molecule, wherein: (1) the first gRNA molecule is: (a) selected from the gRNA molecules of claim 10, or (b) selected from the gRNA molecules of claim 11; and (2) the second gRNA molecule is: (a) selected from the gRNA molecules of claim 13, (b) selected from the gRNA molecules of claim
 14. 105. The composition of any of claims 94-96, comprising a first gRNA molecule and a second gRNA molecule, wherein: (1) the first gRNA molecule is: (a) selected from the gRNA molecules of claim 10, or (b) selected from the gRNA molecules of claim 11; and (2) the second gRNA molecule is: (a) selected from the gRNA molecules of claim 16, (b) selected from the gRNA molecules of claim 17, (c) selected from the gRNA molecules of claim 18, or (d) selected from the gRNA molecules of any of claims 57-68.
 106. The composition of any of claims 94-96, comprising a first gRNA molecule and a second gRNA molecule, wherein: (1) the first gRNA molecule is: (a) selected from the gRNA molecules of claim 13, (b) selected from the gRNA molecules of claim 14; and (2) the second gRNA molecule is: (a) selected from the gRNA molecules of claim 16, (b) selected from the gRNA molecules of claim 17, (c) selected from the gRNA molecules of claim 18, or (d) selected from the gRNA molecules of any of claims 57-68.
 107. The composition of claim 96, comprising a first gRNA molecule and a second gRNA molecule, wherein: (1) the first gRNA molecule is: (a) selected from the gRNA molecules of claim 16, (b) selected from the gRNA molecules of claim 17, (c) selected from the gRNA molecules of claim 18, or (d) selected from the gRNA molecules of any of claims 57-68; and (2) the second gRNA molecule comprises a targeting domain that is complementary to a target sequence of the beta globin gene; or (1) the first gRNA molecule is: (a) selected from the gRNA molecules of claim 4, (b) selected from the gRNA molecules of claim 5, (c) selected from the gRNA molecules of claim 6, (d) selected from the gRNA molecules of claim 7, (e) selected from the gRNA molecules of any of claims 41-56, (f) selected from the gRNA molecules of claim 10, (g) selected from the gRNA molecules of claim 11, (h) selected from the gRNA molecules of claim 13, or (i) selected from the gRNA molecules of claim 14; and (2) the second gRNA molecule comprises a targeting domain that is complementary to a target sequence of the beta globin gene.
 108. The composition of claim 94-96, wherein the first gRNA molecule and the second gRNA molecule are independently selected from the gRNA molecules of any of claims 41-68.
 109. The composition of any of claims 87-108, wherein with respect to the gRNA molecule components of the composition, the composition consists of a first gRNA molecule and a second gRNA molecule.
 110. The composition of any one of claims 87-109, wherein each of said gRNA molecules is in a ribonuclear protein complex (RNP) with a Cas9 molecule described herein, e.g., a Cas9 molecule of any of claim 90 or
 91. 111. The composition of any of claims 87-110, comprising a template nucleic acid, wherein the template nucleic acid comprises a nucleotide that corresponds to a nucleotide at or near the target sequence of the first gRNA molecule.
 112. The composition of any of claim 111, wherein the template nucleic acid comprises nucleic acid encoding: (a) human beta globin, e.g., human beta globin comprising one or more of the mutations G16D, E22A and T87Q, or fragment thereof; or (b) human gamma globin, or fragment thereof.
 113. The composition of any of claims 87-112, formulated in a medium suitable for electroporation.
 114. The composition of any of claims 87-113, wherein each of said gRNA molecules is in a RNP with a Cas9 molecule described herein, and wherein each of said RNP is at a concentration of less than about 10 uM, e.g., less than about 3 uM, e.g., less than about 1 uM, e.g., less than about 0.5 uM, e.g., less than about 0.3 uM, e.g., less than about 0.1 uM.
 115. A nucleic acid sequence that encodes one or more gRNA molecules of any of claims 1-68.
 116. The nucleic acid sequence of claim 115, wherein the nucleic acid comprises a promoter operably linked to the sequence that encodes the one or more gRNA molecules.
 117. The nucleic acid sequence of claim 116, wherein the promoter is a promoter recognized by an RNA polymerase II or RNA polymerase III.
 118. The nucleic acid sequence of claim 117, wherein the promoter is a U6 promoter or an HI promoter.
 119. The nucleic acid sequence of any of claims 115-118, wherein the nucleic acid further encodes a Cas9 molecule.
 120. The nucleic acid sequence of claim 119, wherein the Cas9 molecule comprises any of SEQ ID NO: 6611, SEQ ID NO: 7821, SEQ ID NO: 7822, SEQ ID NO: 7823, SEQ ID NO: 7824, SEQ ID NO: 7825, SEQ ID NO: 7826, SEQ ID NO: 7827, SEQ ID NO: 7828, SEQ ID NO: 7829, SEQ ID NO: 7830, or SEQ ID NO:
 7831. 121. The nucleic acid sequence of any of claims 119-120, wherein said nucleic acid comprises a promoter operably linked to the sequence that encodes a Cas9 molecule.
 122. The nucleic acid sequence of claim 121, wherein the promoter is an EF-1 promoter, a CMV IE gene promoter, an EF-1α promoter, an ubiquitin C promoter, or a phosphoglycerate kinase (PGK) promoter.
 123. A vector comprising the nucleic acid of any of claims 115-122.
 124. The vector of claim 123, wherein in the vector is selected from the group consisting of a lentiviral vector, an adenoviral vector, an adeno-associated viral (AAV) vector, a herpes simplex virus (HSV) vector, a plasmid, a minicircle, a nanoplasmid, and an RNA vector.
 125. A method of altering a cell (e.g., a population of cells), (e.g., altering the structure (e.g., sequence) of nucleic acid) at or near a target sequence within said cell, comprising contacting (e.g., introducing into) said cell (e.g., population of cells) with: 1) one or more gRNA molecules of any of claims 1-68 and a Cas9 molecule; 2) one or more gRNA molecules of any of claims 1-68 and nucleic acid encoding a Cas9 molecule; 3) nucleic acid encoding one or more gRNA molecules of any of claims 1-68 and a Cas9 molecule; 4) nucleic acid encoding one or more gRNA molecules of any of claims 1-68 and nucleic acid encoding a Cas9 molecule; 5) any of 1) to 4), above, and a template nucleic acid; 6) any of 1) to 4) above, and nucleic acid comprising sequence encoding a template nucleic acid; 7) the composition of any of claims 87-114; or 8) the vector of any of claims 123-124.
 126. The method of claim 125, wherein the gRNA molecule or nucleic acid encoding the gRNA molecule, and the Cas9 molecule or nucleic acid encoding the Cas9 molecule, are formulated in a single composition.
 127. The method of claim 125, wherein the gRNA molecule or nucleic acid encoding the gRNA molecule, and the Cas9 molecule or nucleic acid encoding the Cas9 molecule, are formulated in more than one composition.
 128. The method of claim 127, wherein the more than one composition are delivered simultaneously or sequentially.
 129. The method of any of claims 125-128, wherein the cell is an animal cell.
 130. The method of any of claims 125-128, wherein the cell is a mammalian, primate, or human cell.
 131. The method of claim 130, wherein the cell is a hematopoietic stem or progenitor cell (HSPC) (e.g., a population of HSPCs).
 132. The method of any of claims 125-131, wherein the cell is a CD34+ cell.
 133. The method of any of claims 125-132, wherein the cell is a CD34+CD90+ cell.
 134. The method of any of claims 125-133, wherein the cell is disposed in a composition comprising a population of cells that has been enriched for CD34+ cells.
 135. The method of any of claims 125-134, wherein the cell (e.g. population of cells) has been isolated from bone marrow, mobilized peripheral blood, or umbilical cord blood.
 136. The method of any of claims 125-135, wherein the cell is autologous or allogeneic with respect to a patient to be administered said cell.
 137. The method of any of claims 125-136, wherein the altering results in an indel at or near a genomic DNA sequence complementary to the targeting domain of the one or more gRNA molecules.
 138. The method of claim 137, wherein the indel is an indel shown on FIG. 25, Table 15, Table 26, Table 27 or Table
 37. 139. The method of claim 137-138, wherein the indel is an insertion or deletion of less than about 40 nucleotides, e.g., less than 30 nucleotides, e.g., less than 20 nucleotides, e.g., less than 10 nucleotides.
 140. The method of claim 139, wherein the indel is a single nucleotide deletion.
 141. The method of any of claims 137-140, wherein the method results in a population of cells wherein at least about 50%, e.g., at least about 60%, e.g., at least about 70%, e.g., at least about 80%, e.g., at least about 90% (e.g., at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99%) of the cells of the population have been altered, e.g., comprise an indel.
 142. The method of any of claims 125-141, wherein the altering results in a cell (e.g., population of cells) that is capable of differentiating into a differentiated cell of an erythroid lineage (e.g., a red blood cell), and wherein said differentiated cell exhibits an increased level of fetal hemoglobin, e.g., relative to an unaltered cell (e.g., population of cells).
 143. The method of any of claims 125-142, wherein the altering results in a population of cells that is capable of differentiating into a population of differentiated cells, e.g., a population of cells of an erythroid lineage (e.g., a population of red blood cells), and wherein said population of differentiated cells has an increased fraction of F cells (e.g., at least about 15%, at least about 20%, at least about 25%, at least about 30%, or at least about 40% higher) e.g., relative to a population of unaltered cells.
 144. The method of any of claims 125-142, wherein the altering results in a cell that is capable of differentiating into a differentiated cell, e.g., a cell of an erythroid lineage (e.g., a red blood cell), and wherein said differentiated cell produces at least about 6 picograms (e.g., at least about 7 picograms, at least about 8 picograms, at least about 9 picograms, at least about 10 picograms, or from about 8 to about 9 picograms, or from about 9 to about 10 picograms) fetal hemoglobin per cell.
 145. A cell, altered by the method of any of claims 125-144.
 146. A cell, obtainable by the method of any of claims 125-144.
 147. A cell, comprising a first gRNA molecule of any of claims 1-68, or a composition of any of claims 87-114, a nucleic acid of any of claims 115-122, or a vector of any of claims 123-124.
 148. The cell of claim 147, comprising a Cas9 molecule.
 149. The cell of claim 148, wherein the Cas9 molecule comprises any of SEQ ID NO: 6611, SEQ ID NO: 7821, SEQ ID NO: 7822, SEQ ID NO: 7823, SEQ ID NO: 7824, SEQ ID NO: 7825, SEQ ID NO: 7826, SEQ ID NO: 7827, SEQ ID NO: 7828, SEQ ID NO: 7829, SEQ ID NO: 7830, or SEQ ID NO:
 7831. 150. The cell of any of claims 145-149, wherein the cell comprises, has comprised, or will comprise a second gRNA molecule of any of claims 1-68, or a nucleic acid encoding a second gRNA molecule of any of claims 1-68, wherein the first gRNA molecule and second gRNA molecule comprise nonidentical targeting domains.
 151. The cell of any of claims 145-150, wherein expression of fetal hemoglobin is increased in said cell or its progeny (e.g., its erythroid progeny, e.g., its red blood cell progeny) relative to a cell or its progeny of the same cell type that has not been modified to comprise a gRNA molecule.
 152. The cell of any of claims 145-150, wherein the cell is capable of differentiating into a differentiated cell, e.g., a cell of an erythroid lineage (e.g., a red blood cell), and wherein said differentiated cell exhibits an increased level of fetal hemoglobin, e.g., relative to a cell of the same type that has not been modified to comprise a gRNA molecule.
 153. The cell of claim 152, wherein the differentiated cell (e.g., cell of an erythroid lineage, e.g., red blood cell) produces at least about 6 picograms (e.g., at least about 7 picograms, at least about 8 picograms, at least about 9 picograms, at least about 10 picograms, or from about 8 to about 9 picograms, or from about 9 to about 10 picograms) fetal hemoglobin, e.g., relative to a cell of the same type that has not been modified to comprise a gRNA molecule.
 154. The cell of any of claims 145-153, that has been contacted with a stem cell expander.
 155. The cell of claim 154, wherein the stem cell expander is compound 1, compound 2, compound 3, compound 4, or a combination thereof (e.g., compound 1 and compound 4).
 156. The cell of claim 155, wherein the stem cell expander is compound
 4. 157. A cell, e.g., a cell of any of claims 145-156, comprising an indel at or near a genomic DNA sequence complementary to the targeting domain of a gRNA molecule of any of claims 1-68.
 158. The cell of claim 157, wherein the indel is an indel shown on FIG. 25, Table 15, Table 26, Table 27 or Table
 37. 159. The cell of any of claims 157-158, wherein the indel is an insertion or deletion of less than about 40 nucleotides, e.g., less than 30 nucleotides, e.g., less than 20 nucleotides, e.g., less than 10 nucleotides.
 160. The cell of any of claims 157-159, wherein the indel is a single nucleotide deletion.
 161. The cell of any of claims 145-160, wherein the cell is an animal cell.
 162. The cell of claim 161, wherein the cell is a mammalian, a primate, or a human cell.
 163. The cell of any of claims 145-162, wherein the cell is a hematopoietic stem or progenitor cell (HSPC) (e.g., a population of HSPCs).
 164. The cell of any of claims 145-163, wherein the cell is a CD34+ cell.
 165. The cell of claim 164, wherein the cell is a CD34+CD90+ cell.
 166. The cell of any of claims 145-165, wherein the cell (e.g. population of cells) has been isolated from bone marrow, mobilized peripheral blood, or umbilical cord blood.
 167. The cell of any of claims 145-166, wherein the cell is autologous with respect to a patient to be administered said cell.
 168. The cell of any of claims 145-166, wherein the cell is allogeneic with respect to a patient to be administered said cell.
 169. A population of cells comprising the cell of any of claims 145-168.
 170. The population of cells of claim 169, wherein at least about 50%, e.g., at least about 60%, e.g., at least about 70%, e.g., at least about 80%, e.g., at least about 90% (e.g., at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99%) of the cells of the population are a cell according to any one of claims 145-168.
 171. The population of cells of any of claims 169-170, wherein the population of cells is capable of differentiating into a population of differentiated cells, e.g., a population of cells of an erythroid lineage (e.g., a population of red blood cells), and wherein said population of differentiated cells has an increased fraction of F cells (e.g., at least about 15%, at least about 20%, at least about 25%, at least about 30%, or at least about 40% higher) e.g., relative to a population of unmodified cells of the same type.
 172. The population of cells of claim 171, wherein the F cells of the population of differentiated cells produce an average of at least about 6 picograms (e.g., at least about 7 picograms, at least about 8 picograms, at least about 9 picograms, at least about 10 picograms, or from about 8 to about 9 picograms, or from about 9 to about 10 picograms) fetal hemoglobin per cell.
 173. The population of cells of any of claims 169-172, comprising: 1) at least 1e6 CD34+ cells/kg body weight of the patient to whom the cells are to be administered; 2) at least 2e6 CD34+ cells/kg body weight of the patient to whom the cells are to be administered; 3) at least 3e6 CD34+ cells/kg body weight of the patient to whom the cells are to be administered; 4) at least 4e6 CD34+ cells/kg body weight of the patient to whom the cells are to be administered; or 5) from 2e6 to 10e6 CD34+ cells/kg body weight of the patient to whom the cells are to be administered.
 174. The population of cells of any of claims 169-173, wherein at least about 40%, e.g., at least about 50%, (e.g., at least about 60%, at least about 70%, at least about 80%, or at least about 90%) of the cells of the population are CD34+ cells.
 175. The population of cells of claim 174, wherein at least about 10%, e.g., at least about 15%, e.g., at least about 20%, e.g., at least about 30% of the cells of the population are CD34+CD90+ cells.
 176. The population of cells of any of claims 169-175, wherein the population of cells is derived from bone marrow.
 177. The population of cells of any of claims 169-176, wherein the population of cells comprises, e.g., consists of, mammalian cells, e.g., human cells.
 178. The population of cells of any of claims 169-177, wherein the population of cells is autologous relative to a patient to which it is to be administered.
 179. The population of cells of any of claims 169-177, wherein the population of cells is allogeneic relative to a patient to which it is to be administered.
 180. A composition comprising a cell of any of claims 145-168, or the population of cells of any of claims 169-179.
 181. The composition of claim 180, comprising a pharmaceutically acceptable medium, e.g., a pharmaceutically acceptable medium suitable for cryopreservation.
 182. A method of treating a hemoglobinopathy, comprising administering to a patient a cell of any of claims 145-168, a population of cells of any of claims 169-179, or a composition of any of claims 180-181.
 183. A method of increasing fetal hemoglobin expression in a mammal, comprising administering to a patient a cell of any of claims 145-168, a population of cells of any of claims 169-179, or a composition of any of claims 180-181.
 184. The method of claim 182, wherein the hemoglobinopathy is beta-thalassemia or sickle cell disease.
 185. A method of preparing a cell (e.g., a population of cells) comprising: (a) providing a cell (e.g., a population of cells) (e.g., a HSPC (e.g., a population of HSPCs)); (b) culturing said cell (e.g., said population of cells) ex vivo in a cell culture medium comprising a stem cell expander; and (c) introducing into said cell a first gRNA molecule of any of claims 1-68, a nucleic acid molecule encoding a first gRNA molecule of any of claims 1-68, a composition of any of claims 87-114, a nucleic acid of any of claims 115-122, or a vector of any of claims 123-124.
 186. The method of claim 185, wherein after said introducing of step (c), said cell (e.g., population of cells) is capable of differentiating into a differentiated cell (e.g., population of differentiated cells), e.g., a cell of an erythroid lineage (e.g., population of cells of an erythroid lineage), e.g., a red blood cell (e.g., a population of red blood cells), and wherein said differentiated cell (e.g., population of differentiated cells) produces increased fetal hemoglobin, e.g., relative to the same cells which have not been subjected to step (c).
 187. The method of any of claims 185-186, wherein the stem cell expander is compound 1, compound 2, compound 3, compound 4 or a combination thereof (e.g., compound 1 and compound 4).
 188. The method of claim 187, wherein the stem cell expander is compound
 4. 189. The method of any of claims 185-188, wherein the cell culture medium comprises thrombopoietin (Tpo), Flt3 ligand (Flt-3L), and human stem cell factor (SCF).
 190. The method of claim 189, wherein the cell culture medium further comprises human interleukin-6 (IL-6).
 191. The method of claim 189-190, wherein the cell culture medium comprises thrombopoietin (Tpo), Flt3 ligand (Flt-3L), and human stem cell factor (SCF) each at a concentration ranging from about 10 ng/mL to about 1000 ng/mL.
 192. The method of claim 191, wherein the cell culture medium comprises thrombopoietin (Tpo), Flt3 ligand (Flt-3L), and human stem cell factor (SCF) each at a concentration of about 50 ng/mL, e.g, at a concentration of 50 ng/mL.
 193. The method of any of claims 190-192, wherein the cell culture medium comprises human interleukin-6 (IL-6) at a concentration ranging from about 10 ng/mL to about 1000 ng/mL.
 194. The method of claim 193, wherein the cell culture medium comprises human interleukin-6 (IL-6) at a concentration of about 50 ng/mL, e.g, at a concentration of 50 ng/mL.
 195. The method of any of claims 185-194, wherein the cell culture medium comprises a stem cell expander at a concentration ranging from about 1 nM to about 1 mM.
 196. The method of claim 195, wherein the cell culture medium comprises a stem cell expander at a concentration ranging from about 1 uM to about 100 uM.
 197. The method of claim 196, wherein the cell culture medium comprises a stem cell expander at a concentration ranging from about 50 uM to about 75 uM.
 198. The method of claim 197, wherein the cell culture medium comprises a stem cell expander at a concentration of about 50 uM, e.g., at a concentration of 50 uM.
 199. The method of claim 197, wherein the cell culture medium comprises a stem cell expander at a concentration of about 75 uM, e.g., at a concentration of 75 uM.
 200. The method of any of claims 185-199, wherein the culturing of step (b) comprises a period of culturing before the introducing of step (c).
 201. The method of claim 200, wherein the period of culturing before the introducing of step (c) is at least 12 hours, e.g., is for a period of about 1 day to about 3 days, e.g., is for a period of about 1 day to about 2 days, e.g., is for a period of about 2 days.
 202. The method of any of claims 185-201, wherein the culturing of step (b) comprises a period of culturing after the introducing of step (c).
 203. The method of claim 202, wherein the period of culturing after the introducing of step (c) is at least 12 hours, e.g., is for a period of about 1 day to about 10 days, e.g., is for a period of about 1 day to about 5 days, e.g., is for a period of about 2 days to about 4 days, e.g., is for a period of about 2 days or is for a period of about 3 days or is for a period of about 4 days.
 204. The method of any of claims 185-203, wherein the population of cells is expanded at least 4-fold, e.g., at least 5-fold, e.g, at least 10-fold, e.g., relative to cells which are not cultured according to step (b).
 205. The method of any of claims 185-204, wherein the introducing of step (c) comprises an electroporation.
 206. The method of claim 205, wherein the electroporation comprises 1 to 5 pulses, e.g., 1 pulse, and wherein each pulse is at a pulse voltage ranging from 700 volts to 2000 volts and has a pulse duration ranging from 10 ms to 100 ms.
 207. The method of claim 206, wherein the electroporation comprises 1 pulse.
 208. The method of any of claims 206-207, wherein the pulse voltage ranges from 1500 to 1900 volts, e.g., is 1700 volts.
 209. The method of any of claims 206-208, wherein the pulse duration ranges from 10 ms to 40 ms, e.g., is 20 ms.
 210. The method of any of claims 185-209, wherein the cell (e.g., population of cells) provided in step (a) is a human cell (e.g., a population of human cells).
 211. The method of claim 210, wherein the cell (e.g., population of cells) provided in step (a) is isolated from bone marrow, peripheral blood (e.g., mobilized peripheral blood) or umbilical cord blood.
 212. The method of claim 211, wherein the cell (e.g., population of cells) provided in step (a) is isolated from bone marrow, e.g., is isolated from bone marrow of a patient suffering from a hemoglobinopathy.
 213. The method of any of claims 185-212, wherein the population of cells provided in step (a) is enriched for CD34+ cells.
 214. The method of any of claims 185-213, wherein subsequent to the introducing of step (c), the cell (e.g., population of cells) is cryopreserved.
 215. The method of any of claims 185-214, wherein subsequent to the introducing of step (c), the cell (e.g., population of cells) comprises an indel at or near a genomic DNA sequence complementary to the targeting domain of the first gRNA molecule.
 216. The method of any of claim 132, wherein the indel is an indel shown on FIG. 25, Table 15, Table 26, Table 27 or Table
 37. 217. The method of any of claims 185-216, wherein after the introducing of step (c), at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98% or at least about 99% of the cells of the population of cells comprise an indel at or near a genomic DNA sequence complementary to the targeting domain of the first gRNA molecule.
 218. The method of claim 217, wherein the indel in each of said cells of the population of cells is an indel shown in FIG. 25, Table 15, Table 26, Table 27 or Table
 37. 219. A cell (e.g., population of cells), obtainable by the method of any of claims 185-218.
 220. A method of treating a hemoglobinopathy, comprising administering to a human patient a composition comprising a cell (e.g., a population of cells) of claim
 219. 221. A method of increasing fetal hemoglobin expression in a human patient, comprising administering to said human patient a composition comprising a cell (e.g., a population of cells) of claim
 219. 222. The method of claim 220, wherein the hemoglobinopathy is beta-thalassemia or sickle cell disease.
 223. The method of any of claims 220-222, wherein the human patient is administered a composition comprising at least about 1e6 cells of claim 219 per kg body weight of the human patient, e.g., at least about 1e6 CD34+ cells of claim 219 per kg body weight of the human patient.
 224. The method claim 223, wherein the human patient is administered a composition comprising at least about 2e6 cells of claim 219 per kg body weight of the human patient, e.g., at least about 2e6 CD34+ cells of claim 219 per kg body weight of the human patient.
 225. The method claim 223, wherein the human patient is administered a composition comprising from about 2e6 to about 10e6 cells of claim 219 per kg body weight of the human patient, e.g., at least about 2e6 to about 10e6 CD34+ cells of claim 219 per kg body weight of the human patient.
 226. A gRNA molecule of any of claims 1-86, a composition of any of claim 87-114 or 180-181, a nucleic acid of any of claims 115-122, a vector of any of claims 123-124, a cell of any of claim 145-168 or 219, or a population of cells of any of claims 169-179, for use as a medicament.
 227. A gRNA molecule of any of claims 1-86, a composition of any of claim 87-114 or 180-181, a nucleic acid of any of claims 115-122, a vector of any of claims 123-124, a cell of any of claim 145-168 or 219, or a population of cells of any of claims 169-179, for use in the manufacture of a medicament.
 228. A gRNA molecule of any of claims 1-86, a composition of any of claim 87-114 or 180-181, a nucleic acid of any of claims 115-122, a vector of any of claims 123-124, a cell of any of claim 145-168 or 219, or a population of cells of any of claims 169-179, for use in the treatment of a disease.
 229. A gRNA molecule of any of claims 1-86, a composition of any of claim 87-114 or 180-181, a nucleic acid of any of claims 115-122, a vector of any of claims 123-124, a cell of any of claim 145-168 or 219, or a population of cells of any of claims 169-179, for use in the treatment of a disease, wherein the disease is a hemoglobinopathy.
 230. A gRNA molecule of any of claims 1-86, a composition of any of claim 87-114 or 180-181, a nucleic acid of any of claims 115-122, a vector of any of claims 123-124, a cell of any of claim 145-168 or 219, or a population of cells of any of claims 169-179, for use in the treatment of a disease, wherein the hemoglobinopathy is beta-thalassemia or sickle cell disease. 